Multi-target modulation for treating fibrosis and inflammatory conditions

ABSTRACT

The present invention relates to compositions comprising one or more active agents that selectively modulate the expression of two or more genes, for example at the post-transcription level, that are involved in fibrosis and/or inflammatory conditions. Also provided are methods of using such compositions for treating fibrotic diseases, as well as other diseases including inflammatory diseases and cancer.

CROSS-REFERENCE TO RELATED APPLICATION

This patent application claims priority to U.S. Provisional PatentApplication No. 61/648,076, filed May 16, 2012, the disclosure of whichis incorporated herein by reference in its entirety.

TECHNICAL FIELD

This application relates generally to the fields of compositions andmethods for treating fibrosis and inflammatory compositions bymodulating the expression of two or more target genes.

BACKGROUND

Fibrosis is the formation of excess fibrous connective tissue in anorgan or tissue in a reparative or reactive process, in a pathologicalsituation, as opposed to formation of fibrous tissue as a normalconstituent of an organ or tissue. Fibrosis may be the result of chronicinflammatory reactions induced by a variety of stimuli includingpersistent infections, autoimmune reactions, allergic responses,chemical insults, radiation, and tissue injury. Scarring is confluentfibrosis that obliterates the architecture of the underlying organ ortissue. Different organs can be affcctcd by fibrotic diseases,including: Pulmonary fibrosis (lungs); Idiopathic pulmonary fibrosis(where the cause is unknown), Cystic fibrosis (caused by geneticmutation of CFTR gene [cystic fibrosis transmembrane conductanceregulator]); Cirrhosis (liver); Endomyocardial fibrosis (heart);Progressive kidney disease, Mediastinal fibrosis (soft tissue of themediastinum); Myelofibrosis (bone marrow), Retroperitoneal fibrosis(soft tissue of the retroperitoneum); Progressive massive fibrosis(lungs); a complication of coal workers' pneumoconiosis; Nephrogenicsystemic fibrosis (skin), Crohn's Disease (intestine); Keloid (skin);Old myocardial infarction (heart); Scleroderma/systemic sclerosis (skin,lungs); Arthrofibrosis (knee, shoulder, other joints); and some forms ofadhesive capsulitis (shoulder).

Despite having distinct clinical manifestations, most chronic fibroticdisorders have in common a persistent irritant that sustains theproduction of growth factors, proteolytic enzymes, angiogenic factorsand fibrogenic cytokines, which stimulate the deposition of connectivetissue elements that progressively remodel and destroy normal tissuearchitecture [1-3]. In some diseases, such as idiopathic pulmonaryfibrosis, liver cirrhosis, cardiovascular fibrosis, systemic sclerosis,scleroderma and nephritis, extensive tissue remodelling and fibrosis canultimately lead to organ failure and death.

Idiopathic pulmonary fibrosis, scleroderma and liver fibrosis/cirrhosisare serious fibrosis-related diseases that present significant clinicalproblems and unmet medical needs for which to date there are no approvedor effective drugs.

Idiopathic pulmonary fibrosis (IPF): IPF is a progressive and generallyfatal disease characterized by scarring of the lungs that thickens thelung lining, causing an irreversible loss of lung structure andfunction. IPF affects 5 million people worldwide and 130,000-200,000people in the US, with about 48,000 new cases diagnosed and 40,000deaths each year, with medical costs estimated at $2.8 billion per100,000 patients [2, 3]. Median survival is 2-4 years followingdiagnosis, and the 5-year survival is 20-40% [4, 5]. Currently, there isno known cause, no FDA approved treatments and no cure for IPF [6]. IPFpatients typically are treated with anti-inflammatory drugs, includingcorticosteroids and cytotoxic agents, despite the fact that there is noevidence that they have any effect on long-term patient survival.

While drugs currently under investigation for IPF including IFNgamma,Etanercept, Bosentan, and Pirfenidone, QAX576 (IL-13 blocker), FG-3019(CTGF antibody), CNTO-888 (CCL2 antibody), GC-1008 (TGF beta-antibody),Losartan and Thalidomide are directed against targets in the pathologyof IPF, concerns remain about their clinical efficacy as a single agenttherapy due to the redundancy of signaling pathways involved in IPF [6].

Systemic Scleroderma (SS): SS is an autoimmune disorder and a connectivetissue disease that involves changes in the skin, blood vessels,muscles, and internal organs. There are an estimated 300,000 people inthe US who have scleroderma, a third of whom have SS [7]. Local diseaseaffects only skin tissues while SS affects skin and underlying tissues,blood vessels, and major organs including the heart, lungs, or kidneys.In diffuse cutaneous disease, five-year survival is 70%, and 10-yearsurvival is 55% [8]. Currently there is no cure and no specifictreatment for scleroderma, SS treatment includes immunosuppressive andanti-inflammatory drugs including corticosteroids, methotrexate,cyclophosphamide, azathioprine, and mycophenolate [9, 10].

Liver cirrhosis (LC): Liver fibrogenesis is characterized by excessiveaccumulation of extra-cellular matrix (ECM), leading to cirrhosis andcomplications including portal hypertension, liver failure, andhepatocellular carcinoma [11]. LC causes 800,000 deaths worldwideannually [12]. In the US, LC causes 27,000 deaths annually [13].Established cirrhosis has a 10-year mortality of 34-66% [14]. Commoncauses of cirrhosis include alcohol consumption, chronic hepatitis B, Cand D, obesity, toxins, bile duct diseases, and autoimmune hepatitis[15]. Currently there is no treatment available for LC, and health carecosts for managing this disease are high.

Tissue fibrosis is defined by the overgrowth, hardening, and/or scarringof various tissues as a result of excessive deposition of extracellularmatrix (ECM). The key cellular mediator of fibrosis is themyofibroblast, which produces excessive amounts of ECM components suchas collagen when activated (Claman, 1991). Myofibroblasts are generatedfrom a variety of sources including resident mesenchymal cells,epithelial and endothelial cells in processes termedepithelial/endothelial-mesenchymal (EMT/EndMT) transition, as well asfrom circulating fibroblast-like cells called fibrocytes that arederived from bone-marrow stem cells. Myofibroblasts are activated by avariety of mechanisms, including paracrine signals derived fromlymphocytes and macrophages, autocrine factors secreted bymyofibroblasts, and pathogen-associated molecular patterns produced bypathogenic organisms recognized by pattern recognition receptors (i.e.TLRs) on fibroblasts.

The ECM contains 3 major components: structural proteins andproteoglycans, non-structural matricellular proteins, and growthfactors/inflammatory cytokines (Brekken, 2001). Although structuralproteins such as collagens are most prominently increased in fibrotictissues, matricellular proteins and growth factors are believed to bethe major players in the maintenance of homeostasis in the ECM. Numerousstudies have shown that ECM biosynthesis and deposition are regulated bymatricellular proteins and growth factors and by alterations in cell-ECMinteractions that are accompanied by reorganization of the cytoskeletalnetwork (Varedi, 1997).

The progression of fibrotic diseases involves the intricate interplay ofall 3 ECM components. Growth factors, cytokines and chemokines stimulatethe proliferation and activation of lymphocytes, macrophages andmyofibroblasts. Activated myofibroblasts and other cells express highlevels of different ECM proteins, including matricellular proteins andother non-structural proteins, and structural proteins such as collagen,fibronectin, and vitronectin. Cytokines (IL-13, IL-21, TGF-beta1),chemokines (MCP-1, MIP-1beta), angiogenic factors (VEGF), growth factors(PDGF, CTGF), peroxisome proliferator-activated receptors (PPARs), acutephase proteins (SAP), caspases, and components of therenin-angiotensin-aldosterone system (ANG II) have been identified asimportant regulators of fibrosis (Wynn, 2008).

The matricellular and other non-structural proteins play key roles inthe organization and remodeling of ECM. Several such proteins have beenclosely associated with the pathogenesis of fibrosis including SPARC,thrombospondin, CCN1, LOXL2, TGF-beta1, CTGF, and TIMP.

The expression and deposition of ECM proteins in fibrotic diseases areregulated by complicated cascades of cell surface receptors, signalingmolecules, and transcription factors such as Smad 3, Smad 7, SOX9,arrestin.

RNAi is an evolutionarily conserved process of sequence-specific,post-transcriptional gene silencing. RNAi is initiated by dsRNA that ishomologous in sequence to the silenced gene. MicroRNAs (miRNAs) are aclass of endogenous, small, non-coding RNA molecules of ˜22 nucleotidesthat are located in independent noncoding transcripts or in introns ofprotein-coding genes and post-transcriptionally control the translationand stability of mRNAs. Small interfering RNAs (siRNA) aredouble-stranded RNA molecules approximately 21-25 base pairs (bp) longthat act to inhibit gene expression through initiating enzymaticdegradation of a sequence-matched mRNA. miRNAs and siRNAs bind to theRNA-induced silencing complex (RISC), which selectively retains theantisense strand (guide strand) and silences gene expression bydegrading the complementary and corresponding mRNA strand.

While the targeted gene down regulation by RNAi is proposed as apotential therapeutic strategy for a multitude of disease conditions,the safe and effective delivery of RNAi therapeutics remains achallenge. The physicochemical characteristics of siRNA and miRNA (i.e.large molecular weight and anionic charge) prevent passive diffusionacross the plasma membrane of most cell types, and siRNA is prone todegradation in physiological conditions. Therefore a biocompatible,nontoxic and nonimmunogenic carrier is required to deliver siRNA andmiRNA to the target site, which will dramatically improve its clinicalpotential. The current siRNA and miRNA delivery methods include viraltransfection or non-viral techniques including liposomes, dendrimers,linear polymers, polymerosomes, micelles, peptides, nanoparticles, andlocal delivery by electrotransfer.

All references cited herein, including patent applications andpublications, are incorporated by reference in their entirety.

SUMMARY OF THE INVENTION

The present invention provides compositions comprising one or more (suchas two or more) active agents that selectively modulate the expressionof two or more genes, for example at the post-transcription level, thatare involved in fibrosis and/or inflammatory conditions. Also providedare methods of using such compositions for treating fibrotic diseases,as well as other diseases including inflammatory diseases and cancer.

The present invention in some embodiments provides a pharmaceuticalcomposition for preventing or treating fibrosis and other diseasesinvolving chronic inflammation in mammals by targeting 2 or more genesinvolved in the development and progression of fibrosis using one ormore nucleic acids (such as oligonucleotides) including, but not limitedto, antisense oligonucleotides, RNAi (such as shRNAs, siRNAs, miRNAs,antagomirs) and plasmid DNA.

The present invention also provides a pharmaceutical composition totreat fibrosis or inflammatory conditions or diseases, including but notlimited to: pulmonary fibrosis, idiopathic pulmonary fibrosis,progressive massive fibrosis of the lung, cystic fibrosis, mediastinalfibrosis, liver fibrosis, cirrhosis, endomyocardial fibrosis, cardiacfibrosis, old myocardial infarction, progressive kidney disease, renalfibrosis, myelofibrosis, retroperitoneal fibrosis, nephrogenic systemicfibrosis, Crohn's disease, keloids, scleroderma/systemic sclerosis,arthrofibrosis, adhesive capsulitis, fibromyalgia, peritoneal fibrosis,radiation induced fibrosis, burn induced fibrosis, trauma inducedfibrosis, scarring fibrosis, and wound healing fibrosis.

The invention compositions are also useful for wound healing resultingfrom traumatic injury such as burns or for healing of chronic wounds andreducing scarring and fibrosis

The present invention also provides a pharmaceutical composition totreat desmoplastic cancers or cancers having a fibrotic component,including but not limited to: squamous cell carcinomas independent oftheir location, bilio-pancreatic carcinomas, mesothelioma, desmoplasticfibroma, desmoplastic round cell tumor, breast cancer, ovarian cancer,colorectal carcinoma and tumors of gastrointestinal tract, lung cancers,lymphomas, myelofibrosis, leukemias melanoma, brain, tumors (includingglioblastoma, cerebral astrocytoma, neuroblastoma, and medulloblastoma),bladder cancers, hepatocellular and urothelial tumors, and tumors of thepituitary gland.

The present invention provides a pharmaceutical composition thatcomprises multiple (two or more) single stranded or double strandednucleic acids, including antisense oligonucleotides, RNAi, shRNAs,siRNAs, miRNAs, antagomirs or plasmid DNA which inhibits or modulate theactivity or expression of two or more of genes involved in thedevelopment and progression of fibrosis, including but not limited to:CTGF, TGFbetai, TGFbeta receptor 1, TGFbeta receptor 2, TGFbeta reccptor3, beta-catenin, SPARC, VEGF, Angiotensin II, TIMP, HSP47,thrombospondin, CCN1, LOXL2, MMP2, MMP9, CCL2, Adenosine receptor A2A,Adenosine receptor A2B, Adenylyl cyclase, Smad 3, Smad 4, Smad 7, SOX9,arrestin, PDCD4, PAI-1, NF-kB, and PARP-1 GAD65, sGAD65, BAX, p53 PTEN,STAT5, smoothened, GUI1, GLI2, and Patched-1. Yet another gene ofinterest for the present invention is HIF-1 alpha.

The present invention provides a pharmaceutical composition in whichmultiple (two or more) single stranded or double stranded nucleic acidsincluding antisense oligonucleotides, shRNAs, siRNAs, miRNAs,antagomirs, plasmid DNA, etc. are covalently conjugated to, ornon-covalently associated with, or formulated with peptides, proteins,antibodies, lipids, phospholipids, polymers, aptamers, nanoparticlcs,liposomes, dendrimers, polymcrosomes, viral vectors, and micelles. Sucha composition is suitable for mammalian and human use.

The present invention provides a method of treatment and a method toadminister to human and other mammals an effective amount of apharmaceutical composition once or multiple times to treat fibrosis andother inflammatory conditions or diseases by systemic or localadministration. The administration routes include but are not limitedto: oral, intravenous, intraarterial, intracardiac, intracatheter,intraperitoneal, intravesical, transdermal, nasal inhalation, pulmonarydelivery, intracavity, intracranial, intrathecal, subcutaneous,intradermal, intramuscular, intraocular, topical, rectal, vaginal,direct injection/administration, and local delivery with electrotransferor microneedle injection.

In one preferred embodiment, the single stranded or double strandednucleic acids including antisense oligonucleotides, shRNAs, siRNAs,miRNAs, antagomirs, plasmid DNA etc. are encapsulated in a peptide-basednanoparticle and administered via intravenous systemic administration.

Invention compositions maybe prepared in powder form, liquid form,tablet or capsule form, in the form of gels, creams, ointments, sprays,embedded in wound dressings or dissolving strips and are suitable foradministration by the methods described above

Devices used for delivery can include delivery through a needle,microneedle, convection enhanced delivery device, catheters,intravesical urinary catheters, aerosol, inhaler, nasal spray, pessary,suppository, single use or repeat use devices, creams, ointments,patches, etc.

The present invention comprises a method to select effectivecombinations of 2 or more gene targets or corresponding expressedproteins for down regulation or modulation. These gene targets can beselected from different aspects implicated in the development offibrosis, including but not limited to ECM components (structuralproteins and proteoglycans, non-structural matricellular proteins, andgrowth factors/inflammatory cytokines), and cellular components offibroblasts (receptors for growth factors/inflammatory cytokines, signaltransduction molecules such as kinases, enzymes, and adaptor proteins,transcription factors, and other cellular components regulating theproliferation, metabolism, survival, migration, and differentiation offibroblasts).

DETAILED DESCRIPTION

In recent years, multiple proteins have been implicated as potential keyregulators promoting pathogenesis of fibrotic diseases, and some studieshave suggested that targeted down regulation of an individual genethrough the RNAi approach could have therapeutic effect againstfibrosis. However, little effort has been made to develop a multi-targetRNAi (shRNA, siRNA and/or miRNA,) or plasmid DNA therapeutics to preventand treat fibrotic diseases by inhibiting the expression of two or moregenes involved in fibrosis. The present invention provides a therapeutic(for example a composition comprising multiple nucleic acids such asoligonucleotides, particularly siRNA or miRNA molecules) aiming for thecombined inhibition of two or more target genes involved in fibrosis.

The present invention thus in some embodiments relates to the use of acombination of multiple single or double stranded nucleic acids (such asantisense oligonucleotides, RNAi, shRNAs, siRNAs, miRNAs, antagomirs andplasmid DNA) for selectively modulating (such as inhibiting) theexpression of two or more genes, for example at the post-transcriptionlevel, whereas these genes controls the same or distinct signalingpathways and cellular procedures, and play essential roles in thepathology and progression of fibrosis diseases affecting differentorgans. The invention also provides the methods of composition anddelivering the combination of nucleic acids (such as oligonucleotides)to the fibrotic disease sites in target organs, including the use of anovel peptide-based nanoparticle oligonucleotide delivery vehicle as acarrier of the combination of oligonucleotide compounds for thetreatment of fibrotic diseases. The invention also describes thetherapeutic use of such compositions containing oligonucleotidecompounds to treat patients with fibrotic diseases, as well as otherdiseases including inflammatory diseases and cancer.

In some embodiments, the composition comprises two or more active agentsin a predetermined ratio. This allows simultaneous delivery of multipleactive agents, which may modulate the expression of different targets.The predetermined ratio can be selected so as to allow the mosteffective delivery and/or target modulation.

The present application therefore in one aspect provides apharmaceutical composition comprising one or more nucleic acids (such asoligonucleotides) that specifically target the expression of two or moregenes involved in the development or progression of fibrosis orinflammation. In another aspect, there is provided a pharmaceuticalcomposition comprising one or more active agents that modulate theactivity or expression of two or more genes involved in the developmentand progression of fibrosis or inflammation, selected from, CTGF(CCN2),TGFbetai, TGFbeta receptor 1, TGFbeta receptor 2, TGFbeta receptor 3,beta-catenin, SPARC, VEGF, Angiotensin II, TIMP, HSP47, thrombospondin,CCN1, LOXL2, MMP2, MMP9, CCL2, Adenosine receptor A2A, Adenosinereceptor A2B, Adenylyl cyclase, Smad 3, Smad 4, Smad 7, SOX9, arrestin,PDCD4, PAI-1, NF-kB, and PARP-1 GAD65, sGAD65, BAX, p53 PTEN, STAT5 andrelevant genes in the hedgehog pathway—smoothened, GLI1, GLI2, andPatched-1. Yet another gene of interest for the present invention isHIF-1alpha.

In another aspect, there is provided a method of treating a fibrotic orinflammatory condition in an individual comprising administering to saidindividual an effective amount of any of the pharmaceutical compositiondescribed herein. Also provided are kits, unit dosages, and articles ofmanufacture useful for the methods described herein.

It is understood that aspect and embodiments of the invention describedherein include “consisting” and/or “consisting essentially of” aspectsand embodiments.

As used herein, the singular form “a”, “an”, and “the” includes pluralreferences unless indicated otherwise.

As is understood by one skilled in the art, reference to “about” a valueor parameter herein includes (and describes) embodiments that aredirected to that value or parameter per se. For example, descriptionreferring to “about X” includes description of “X”.

I. Methods and Compositions of the Present Invention

In some embodiments, there is provided a method of treating a fibroticor inflammatory condition in an individual, comprising administering tothe individual an effective amount of a pharmaceutical compositioncomprising one or more (such as any of 2, 3, 4, 5, 6, 7, or 8) nucleicacids (for example single-stranded or double-stranded oligonucleotides)that modulate the expression of two or more genes involved in thedevelopment or progression of fibrosis or inflammation. In someembodiments, the two or more genes are selected from the groupconsisting of CTGF(CCN2), TGFbetai, TGFbeta receptor 1, TGFbeta receptor2, TGFbeta receptor 3, beta-catenin, SPARC, VEGF, Angiotensin II, TIMP,HSP47, thrombospondin, CCN1, LOXL2, MMP2, MMP9, CCL2, Adenosine receptorA2A, Adenosine receptor A2B, Adenylyl cyclase, Smad 3, Smad 4, Smad 7,SOX9, arrestin, PDCD4, PAI-1, NF-kB, and PARP-1 GAD65, sGAD65, BAX, p53PTEN, STAT5, and relevant genes in the hedgehog pathway—smoothened,GLI1, GLI2, and Patched-1. Yet another gene of interest for the presentinvention is HIF-1 alpha. In some embodiments, at least one of thenucleic acids is selected from the group consisting of antisenseoligonucleotide, RNAi, shRNA, siRNA, miRNA, or plasmid DNA.

In some embodiments, there is provided a method of treating a fibroticor inflammatory condition in an individual, comprising administering tothe individual an effective amount of a pharmaceutical compositioncomprising one or more (such as any of 2, 3, 4, 5, 6, 7, or 8) activeagents (such as nucleic acids, for example, single-stranded ordouble-stranded oligonucleotides) that modulate the activity orexpression of two or more genes involved in the development andprogression of fibrosis or inflammation, selected from, CTGF(CCN2),TGFbetai, TGFbeta receptor 1, TGFbeta receptor 2, TGFbeta receptor 3,beta-catenin, SPARC, VEGF, Angiotensin II, TIMP, HSP47, thrombospondin,CCN1, LOXL2, MMP2, MMP9, CCL2, Adenosine receptor A2A, Adenosinereceptor A2B, Adenylyl cyclase, Smad 3, Smad 4, Smad 7, SOX9, arrestm,PDCD4, PAI-1, NF-kB, and PARP-1 GAD65, sGAD65, BAX, p53 PTEN, STAT5, andrelevant genes in the hedgehog pathway—smoothened, GLI1, GLI2, andPatched-1. Yet another gene of interest for the present invention isHIF-1alpha. In some embodiments, at least one of the active agents is aprotein (such as an antibody). In some embodiments, at least one of theactive agents is a small molecule. In some embodiments, at least one ofthe active agents is an oligonucleotide, in some embodiments, the twoactive agents are of the same kind. In some embodiments, the two activeagents are of different kinds.

In some embodiments, there is provided a method of treating a flbroticor inflammatory condition in an individual, comprising administering tothe individual an effective amount of a pharmaceutical compositioncomprising one or more (such as any of 2, 3, 4, 5, 6, 7, or 8) RNAi (forexample siRNA or shRNA) that modulate the expression of two or moregenes involved in the development or progression of fibrosis orinflammation. In some embodiments, the two or more genes are selectedfrom the group consisting of CTGF(CCN2), TGFbetai, TGFbeta receptor 1,TGFbeta receptor 2, TGFbeta receptor 3, beta-catenin, SPARC, VEGF,Angiotensin II, TIMP, HSP47, thrombospondin, CCN1, LOXL2, MMP2, MMP9,CCL2, Adenosine receptor A2A, Adenosine receptor A2B, Adenylyl cyclase,Smad 3, Smad 4, Smad 7, SOX9, arrestin, PDCD4, PAI-1, NF-kB, and PARP-1GAD65, sGAD65, BAX, p53 PTEN, STAT5, and relevant genes in the hedgehogpathway—smoothened, GLI1, GLI2, and Patched-1. Yet another gene ofinterest for the present invention is HIF-1alpha. In some embodiments,the nucleic acids are about 10 to about 50 nucleotides long. In someembodiments, the two or more nucleic acids are of the same kind. In someembodiments, the two or more nucleic acids are of different kinds.

The fibrotic or inflammatory condition described herein in someembodiments is selected from the group consisting of pulmonary fibrosis,idiopathic pulmonary fibrosis, progressive massive fibrosis of the lung,cystic fibrosis, mediastinal fibrosis, liver fibrosis, cirrhosis,endomyocardial fibrosis, cardiac fibrosis, old myocardial infarction,progressive kidney disease, renal fibrosis, myelofibrosis,retroperitoneal fibrosis, nephrogenic systemic fibrosis, Crohn'sdisease, keloids, scleroderma/systemic sclerosis, arthrofibrosis,adhesive capsulitis, fibromyalgia, peritoneal fibrosis, radiationinduced fibrosis, burn induced fibrosis, trauma induced fibrosis,scarring fibrosis, and wound healing fibrosis. In some embodiments, thefibrotic or inflammatory conditions is a desmoplastic cancer, whereinthe desmoplastic cancer is selected from the group consisting of:squamous cell carcinoma independent of their location, bilio-pancreaticcarcinoma, mesothelioma, desmoplastic fibroma, desmoplastic round celltumor, breast cancer, ovarian cancer, colorectal carcinoma and tumor ofgastrointestinal tract, lung cancer, lymphoma, myelofibrosis, leukemia,melanoma, brain tumor (including glioblastoma, cerebral astrocytoma,neuroblastoma, and medulloblastoma), bladder cancer, hepatocellular andurothelial tumor, and tumor of the pituitary gland. The pharmaceuticalcomposition can be administered by any of suitable route, including, butnot limited to, oral, intravenous, intraarterial, intracardiac,intracatheter, intraperitoneal, intravesical, transdermal, nasalinhalation, pulmonary delivery, intracavity, intracranial, intrathecal,subcutaneous, intradermal, intramuscular, intraocular, topical, rectal,vaginal, direct injection/administration, or local delivery withelectrotransfer or microneedle injection.

In some embodiments according to any one of the methods described above,the individual for treatment is selected based on the expression levelof at least one genes involved in the development and progression offibrosis or inflammation. In some embodiments, the method furthercomprises determining the expression level of at least one gene prior tothe administration of the pharmaceutical composition.

“Modulation” of activity or expression means regulating or altering thestatus or copy numbers of a gene or mRNA or changing the amount of geneproduct such as a protein that is produced. In some embodiments, theactive agent inhibits the expression of the target gene. In someembodiments, the modulation (such as inhibition) occurs at apost-transcriptional level. In some embodiments, the active agentinhibits the expression of the gene or gene product by at least aboutany of 10%, 20%, 30%, 40%, 60%, 70%, 80%, 90%, or 100%. In someembodiments such as in the case of Plasmid delivery, the active agentmay increase the expression of the gene or gene product by at leastabout any of 10%, 20%, 30%, 40%, 60%, 70%, 80%, 90%, or 100%.

In another aspect, there are provided pharmaceutical compositionscomprising two or more (such as any of 2, 3, 4, 5, 6, 7, or 8) activeagents (such as nucleic acids, for example single-stranded ordouble-stranded oligonucleotides) that modulate the expression of two ormore genes involved in the development or progression of fibrosis orinflammation, including, but not limited to, CTGF(CCN2), TGFbetai,TGFbeta receptor 1, TGFbeta receptor 2, TGFbeta receptor 3,beta-catenin, SPARC, VEGF, Angiotensin II, TIMP, HSP47, thromhospondin,CCN1, LOXL2, MMP2, MMP9, CCL2, Adenosine receptor A2A, Adenosinereceptor A2B, Adenylyl cyclase, Smad 3, Smad 4, Smad 7, SOX9, arrestin,PDCD4, PAI-1, NF-kB, and PARP-1 GAD65, sGAD65, BAX, p53 PTEN, STAT5, andrelevant genes in the hedgehog pathway—smoothened, GLI1, GLI2, andPatched-1. Yet another gene of interest for the present invention isHIF-1 alpha. These pharmaceutical compositions described herein areuseful for any one of the methods described herein. In some embodiments,the two or more active agents are of the same kind. In some embodiments,the two or more active agents are of different kinds. In someembodiments, the pharmaceutical composition comprises two active agents,and wherein the molar ratio of the two active agents is about 0.1:1 toabout 10:1. In some embodiments, the two or more active agents in thepharmaceutical composition are in equal molar proportions.

In some embodiments, there are provided pharmaceutical compositionscomprising two or more (such as any of 2, 3, 4, 5, 6, 7, or 8) RNAi(such as siRNA or shRNA) that modulate the expression of two or moregenes involved in the development or progression of fibrosis orinflammation, including, but not limited to, CTGF(CCN2), TGFbetai,TGFbeta receptor 1, TGFbeta receptor 2, TGFbeta receptor 3,beta-catenin, SPARC, VEGF, Angiotensin II, TIMP, HSP47, thrombospondin,CCN1, LOXL2, MMP2, MMP9, CCL2, Adenosine receptor A2A, Adenosinereceptor A2B, Adenylyl cyclase, Smad 3, Smad 4, Smad 7, SOX9, arrestin,PDCD4, PAI-1, NF-kB, and PARP-1 GAD65, sGAD65, BAX, p53 PTEN, STAT5, andrelevant genes in the hedgehog pathway—smoothened, GLI1, GLI2, andPatched-1. In some embodiments, the two interfering RNAs are of the samekind. In some embodiments, the two or more interfering RNAs are ofdifferent kinds. In some embodiments, the pharmaceutical compositioncomprises two interfering RNAs, and wherein the molar ratio of the twoactive agents is about 0.1:1 to about 10:1. In some embodiments, the twoor more interfering RNAs in the pharmaceutical composition are in equalmolar proportions.

The nucleic acids described in any of the embodiments above can be ofany length between about 12 to about 100 nucleotides long, including forexample about any of 15-80, 18-60, 20-50, or 25-30nucleotides long. Insome embodiments, the nucleic acids are at least about 60% (includingfor example at least about any of 70%, 80%, 90%, 95%, 98%, or 99%)identical to the corresponding target gene. Tn some embodiments, thenucleic acids are modified, for example by incorporating non-naturallyoccurring nucleotides.

The active agents (such as nucleic acids) described in any of theembodiments above can be associated (such as covalently ornon-covalently associated) with a carrier molecule, which can include,but are not limited to, a peptide, a protein, an antibody, a lipid, aphospholipid, a polymer, an aptamer, a nanoparticle, a liposome, adendrimer, a polymerosome, a viral vector, a micelle or syntheticcompositions including of any of the above that can interact with thewith the active agents through charge interactions and/or hydrophobicinteractions, e.g. a molecule containing charged species and a lipid, ora molecule containing a charged peptide and a lipid. In someembodiments, the carrier molecule is a peptide (such as acell-penetrating peptide, for example a polycationic peptide or anamphipathic peptide). Suitable cell-penetrating peptides include, butare not limited to, a PTD-based peptide, an amphipathic peptide, apoly-arginine-based peptide, a MPG peptide, a CADY peptide, or a Pep-1or Pep-2, peptide. In some embodiments, the composition comprises two ormore different types of peptides (such as different types ofcell-penetrating peptides). For example, in some embodiments, thecomposition comprises both polycationic peptide and amphipathic peptide.In some embodiments, the composition comprises a MPG peptide and a CADYpeptide. Other combinations of the carrier peptides are alsocontemplated.

The nucleic acids and the cell-penetrating peptide in some embodimentscan be present in a complex. In some embodiments, the nucleic acids andthe cell-penetrating peptides are present in nanoparticles comprisingthe complexes of the nucleic acids and the cell-penetrating peptide. Theaverage size of the nanoparticles can be between any of about 30 nm andabout 10 microns, including for example between about 50 nm and about 1micron, between about 50 nm and about 400 nm. The molar ratio of thecell-penetrating peptide and the nucleic acids in the composition can beabout 100:1 to about 1:50, including about any of 50:1 to 1:20, 20:1 to1:10, and the like.

The compositions and methods described in this section are furtherdescribed below in more detail.

II. Pharmaceutical Compositions Comprising two or more Active Agents

Active agents described herein include nucleic acid based molecules suchas oligonucleotides, nucleic acids, polynucleotides, single or doublestranded oligo and polynucleotides, antisense oligonucleotides,different forms of RNAi such as siRNA, shRNA, etc., microRNA (miRNA),antagomirs, ribozyme, aptamer, plasmid DNA, etc. and suitablecombinations of one or more of these agents. In addition, active agentsmay also include proteins such as enzymes or antibodies having aspecific desired effect or small molecules with desired specificactivity. Also contemplated are combinations of nucleic acid basedagents with proteins or small molecules that are either covalentlyattached to each other or provided without any covalent attachment assuitable combinations.

Target genes: Specific and preferred active agents and their targetsinclude those that are directed towards fibrosis and inflammation. Theseinclude agents directed to CTGF(CCN2), TGFbetai, TGFbeta receptor 1,TGFbeta receptor 2, TGFbeta receptor 3, beta-catenin, SPARC, VEGF,Angiotensin II, TIMP, HSP47, thrombospondin, CCN1, LOXL2, MMP2, MMP9,CCL2, Adenosine receptor A2A, Adenosine receptor A2B, Adenylyl cyclase,Smad 3, Smad 4, Smad 7, SOX9, arrestin, PDCD4, PAI-1, NF-kB, and PARP-1GAD65, sGAD65, BAX, p53 PTEN, and STAT5, and relevant genes in thehedgehog pathway—smoothened, GLI1, GLI2, and Patched-1. Yet another geneof interest for the present invention is HIF-1alpha. The specific agentsof interest acting on these targets include nucleic acid basedmolecules, proteins, enzymes or antibodies, and small molecules andtheir combinations as described above. Most preferred are compositionswhich contain more than one active agent thereby having the ability tosimultaneously affect or modulate more than one target related tofibrosis or inflammation.

Preferred molecular targets and key signaling pathways implicated in thepathology of fibrotic diseases, such as Idiopathic Pulmonary Fibrosis,Systemic Scleroderma, and Liver Cirrhosis include transforming growthfactor (TGF)-beta and its receptors, connective tissue growth factor(CTGF), adenosine receptors, SPARC (secreted protein acidic and rich incysteine) and tissue inhibitors of metalloproteinases (TIMPs), which areinvolved in the activation of fibroblasts, inflammatory responses, ECMdeposition, and tissue repair.

The active agent(s) described herein may modulate the expression of twoor more genes in the same signaling pathway, or they modulate theexpression of two or more genes in different pathways. For example, insome embodiments, the active agent (such as nucleic acids, for exampleRNAi) modulates the expression of the TGF-beta signaling pathway. Insome embodiments, the active agent (such as nucleic acids, for exampleRNAi) modulate the expression of the CTGF signaling pathway. In someembodiments, the active agent (such as nucleic acid, for example RNAi)modulates the expression of a protein involved in the hedgehog pathway(which includes, but is not limited to, Patched-1, smoothened, GLI1,GLI-2). In some embodiments, the active agent (such as nucleic acid, forexample RNAi) modulates the expression of an ECM protein (whichincludes, but is not limited to, collagen, fibronectin, andvitronectin). In some embodiments, the active agent (such as nucleicacid, for example RNAi) modulates the expression of a non-structuralprotein involved in the organization and remodeling of the ECM (whichincludes, but is not limited to, SPARC, thrombospondin, CCN1, LOXL2,TGF-beta-1, CTGF, and TIMP). In some embodiments, the active agent (suchas nucleic acid, for example RNAi) modulates the expression of aregulator of fibrosis (which includes, but is not limited to, cytokines,chemokines, angiogenic factors, growth factors, PPAPs, SAP, caspases,and components of the renin- angiotensin-aldosterone system (ANG II).

In some embodiments, the active agent(s) modulate the expressions of twoor more targets proteins in the same signaling transduction pathway. Insome embodiments, the active agent(s) modulate the expression of targetproteins in two or more different signal transduction pathways. Theactive agent(s) can modulate any combinations of the targets describedabove. For example, In some embodiments, the active agent (such asnucleic acid, for example RNAi) modulates the expression of both theTGF-beta signaling pathway and the CTGF pathway or both the SPARC andthe CTGF pathway. Other target combinations include, but are not limitedto, the transforming growth factor (TGF)-beta receptors 1 or 2 withCTGF, transforming growth factor (TGF)-beta receptors 1 or 2 with SPARC,transforming growth factor (TGF)-beta receptors 1 or 2 with Adenosinereceptors, transforming growth factor (TGF)-beta receptors 1 or 2 withTIMPs, SPARC with CTGF, SPARC with Adenosine receptors, SPARC withTIMPs, CTGF with Adenosine receptors, CTGF with TIMPs, Adenosinereceptors with TIMPs, Triple combinations of targets include any of thedouble combinations indicated above with additional single targetsmentioned above.

In some embodiments, at least one of target genes is a gene involved inthe TGF-beta signaling pathway, including TGF-beta. The action ofTGF-beta is characterized by increased production of ECM components, aswell as mesenchymal cell proliferation, differentiation, migration, andaccumulation [16, 17], TGF-beta also induces production of CTGF, whichpromotes fibrogenesis and causes nodular fibrosis in the liver [18, 19].In lung fibroblasts, TGF-beta up regulates the expression of SPARC,which is a key modulator of ECM organization and overexpressed in IPF[20].

In some embodiments, at least one of target genes is a gene involved inthe CTGF signaling pathway, including CTGF. CTGF is involved inradiation-induced fibrosis, lung fibrosis, and scleroderma [18].Transgenic mice overexpressing CTGF in fibroblasts display multiorganfibrosis similar to fibrosis observed with scleroderma [21, 22]. CTGFsiRNA reduce mRNA and protein levels of SPARC, CTGF, Collagen 1 andTGF-beta 1 in fibroblasts in vitro, and attenuates bleomycin inducedfibrosis in skin and lungs [23].

In some embodiments, at least one of target genes is a gene involved inthe adenosine signaling pathway, including adenosine receptors A2A andA2B. Adenosine and its receptors A2A and A2B in pathological conditionspromote fibrosis in the skin, lungs, and liver [24], A2B receptoroverexpression is observed in surgical lung biopsies from severe chronicobstructive pulmonary disease (COPD) and IPF patients [25]. Adenosine,by acting at A2A receptors, stimulates hepatic stellate cell-mediatedfibrosis of the liver by increasing production of collagen I and III[26, 27].

In some embodiments, at least one of target genes is a gene involved inthe SPARC signaling pathway, including SPARC. SPARC, a matricellularprotein, promotes fibrogenesis in IPF, scleroderma, and liver fibrosis[28-30]. SPARC is a key downstream mediator of TGF-beta1 activity [31],and its expression is up regulated by TGF-beta via the PI3k signalingpathway in IPF fibroblasts [20]. SPARC in turn also regulates theexpression of TGF-beta1 [32]. Skin and lung fibrosis induced bybleomycin in mice was markedly reduced by SPARC siRNA delivered bysubcutaneous injection and intratracheal instillation, respectively[29]. Liver fibrosis in rats treated with thiocetamide was significantlyattenuated by treatment with SPARC antisense [33].

In some embodiments, at least one of target genes is a gene involved inthe TIMP (tissue inhibitors of metalloproteinase) signaling pathway,including TIMP. Tissue inhibitors of metalloproteinases (TIMPs) are theendogenous inhibitors of the matrix metalloproteinase families. TIMP-1inhibits the majority of the MMPs while TIMP-3 inhibits all knowninterstitial and membrane-bound MMPs [34]. TIMPs play a pivotal role inliver fibrogenesis [35], and lung tissue samples from IPF patientsdisplay high expression of TIMPs, supporting the hypothesis that TIMPscontribute to a nondegrading fibrillar collagen microenvironment [36].

The methods and compositions described herein allow for modulation ofthe expression of two or more target genes. Exemplary targetcombinations include, but are not limited to, the transforming growthfactor (TGF)-beta receptors 1 or 2 with CTGF, transforming growth factor(TGF)-beta receptors 1 or 2 with SPARC, transforming growth factor(TGF)-beta receptors 1 or 2 with Adenosine receptors, transforminggrowth factor (TGF)-beta receptors 1 or 2 with TIMPs. SPARC with CTGF,SPARC with Adenosine receptors, SPARC with TIMPs, CTGF with Adenosinereceptors, CTGF with TIMPs, Adenosine receptors with TIMPs, Triplecombinations of targets include any of the double combinations indicatedabove with additional single targets mentioned above.

Nucleic acids: In some embodiments, the active agents present in thepharmaceutical compositions are nucleic acids (such asoligonucleotides).

“Polynucleotide,” or “nucleic acid,” as used interchangeably herein,refer to polymers of nucleotides of any length, and include DNA and RNA.The nucleotides can be deoxyribonucleotides, ribonucleotides, modifiednucleotides or bases, and/or their analogs, or any substrate that can beincorporated into a polymer by DNA or RNA polymerase. A polynucleotidemay comprise modified nucleotides, such as methylated nucleotides andtheir analogs. The term “nucleic acid” as used herein refers to apolymer containing at least two deoxyribonueleotidcs or ribonucleotidesin either single- or double-stranded form and includes DNA and RNA. DNAmay be in the form of, e.g., antisense molecules, plasmid DNA,pre-condensed DNA, a PCR product, vectors (P1, PAC, BAC, YAC, artificialchromosomes), expression cassettes, chimeric sequences, chromosomal DNA,or derivatives and combinations of these groups. RNA may be in the formof siRNA, asymmetrical interfering RNA (aiRNA), micro RNA (miRNA), mRNA,tRNA, rRNA, tRNA, viral RNA (vRNA), and combinations thereof. Nucleicacids include nucleic acids containing known nucleotide analogs ormodified backbone residues or linkages, which are synthetic, naturallyoccurring, and non-naturally occurring, and which have similar bindingproperties as the reference nucleic acid. Examples of such analogsinclude, without limitation, phosphorothioates, phosphoramidates, methylphosphonates, chiral-methyl phosphorates, 2′-O-methyl ribonucleotides,and peptide-nucieic acids (PNAs). Unless specifically limited, the termencompasses nucleic acids containing known analogues of naturalnucleotides that have similar binding properties as the referencenucleic acid. Unless otherwise indicated, a particular nucleic acidsequence also implicitly encompasses conservatively modified variantsthereof (e.g., degenerate codon substitutions), alleles, orthologs,SNPs, and complementary sequences as well as the sequence explicitlyindicated. Specifically, degenerate codon substitutions may be achievedby generating sequences in which the third position of one or moreselected (or all) codons is substituted with mixed-base and/ordeoxyinosine residues (Batzer et al., Nucleic Acid Res., 19:5081 (1991);Ohtsuka et al., J. Biol. Chem., 260:2605-2608 (1985); Rossolini et al.,Mol. Cell. Probes, 8:91-98 (1994 s). “Nucleotides” contain a sugardeoxyribose (DNA) or ribose (RNA), a base, and a phosphate group.Nucleotides are linked together through the phosphate groups. “Bases”include purines and pyrimidines, which further include natural compoundsadenine, thymine, guanine, cytosine, uracil, inosine, and naturalanalogs, and synthetic derivatives of purines and pyrimidines, whichinclude, but are not limited to, modifications which place new reactivegroups such as, but not limited to, amines, alcohols, thiols,carboxylates, and alkylhalides. “Oligonucleotide,” as used herein,generally refers to short, generally synthetic polynucleotides that aregenerally, but not necessarily, less than about 200 nucleotides inlength. The terms “oligonucleotide” and “polynucleotide” are notmutually exclusive. The description above for polynucleotides is equallyand fully applicable to oligonucleotides.

In some embodiments, the nucleic acids are single strandedoligonucleotides. In some embodiments, the nucleic acids are doublestranded oligonucleotides. The nucleic acids described herein may be anyof a range of length of up to, but not necessarily 200 nucleotides inthe case of antisense oligonucleotides, RNAi, siRNA, shRNA, miRNA,antagomirs or up to 1000 kilo bases in the case of Plasmid DNA.

In some embodiments, the nucleic acids are interference RNA, such assiRNA or shRNA. “The term “interfering RNA” or “RNAi” or “interferingRNA sequence” refers to single-stranded RNA (e.g., mature miRNA) ordouble-stranded RNA (i.e., duplex RNA such as siRNA, aiRNA, orpre-miRNA) that is capable of reducing or inhibiting the expression of atarget gene or sequence (e.g., by mediating the degradation orinhibiting the translation of mRNAs which are complementary to theinterfering RNA sequence) when the interfering RNA is in the same cellas the target gene or sequence. Interfering RNA thus refers to thesingle-stranded RNA that is complementary to a target mRNA sequence orto the double-stranded RNA formed by two complementary strands or by asingle, self-complementary strand. Interfering RNA may have substantialor complete identity to the target gene or sequence, or may comprise aregion of mismatch (i.e., a mismatch motif). The sequence of theinterfering RNA can correspond to the full-length target gene, or asubsequence thereof. Interfering RNA includes “small-interfering RNA” or“siRNA,” e.g., interfering RNA of about 15-60, 15-50, or 15-40 (duplex)nucleotides in length, more typically about 15-30, 15-25, or 19-25(duplex) nucleotides in length, and is preferably about 20-24, 21-22, or21-23 (duplex) nucleotides in length (e.g., each complementary sequenceof the double-stranded siRNA is 15-60, 15-50, 15-40, 15-30, 15-25, or19-25 nucleotides in length, preferably about 20-24, 21-22, or 21-23nucleotides in length, and the double-stranded siRNA is about 15-60,15-50, 15-40, 15-30, 15-25, or 19-25 base parrs in length, preferablyabout 18-22, 19-20, or 19-21 base pairs in length). siRNA duplexes maycomprise 3′ overhangs of about 1 to about 4 nucleotides or about 2 toabout 3 nucleotides and 5′ phosphate termini. Examples of siRNA include,without limitation, a double-stranded polynucleotide molecule assembledfrom two separate stranded molecules, wherein one strand is the sensestrand and the other is the complementary antisense strand: adouble-stranded polynucleotide molecule assembled from a single strandedmolecule, where the sense and antisense regions are linked by a nucleicacid-based or non-nucleic acid-based linker; a double-strandedpolynucleotide molecule with a hairpin secondary structure havingself-complementary sense and antisense regions; and a circularsingle-stranded polynucleotide molecule with two or more loop structuresand a stem having self-complementary sense and antisense regions, wherethe circular polynucleotide can be processed in vivo or in vitro togenerate an active double-stranded siRNA molecule. Preferably, siRNA arechemically synthesized. siRNA can also be generated by cleavage oflonger dsRNA (e.g., dsRNA greater than about 25 nucleotides in length)with the E. coli RNase III or Dicer. These enzymes process the dsRNAinto biologically active siRNA (see, e.g., Yang et al., Proc. Natl.Acad. Sci. USA, 99:9942-9947 (2002); Calegari et al., Proc. Natl. Acad.Sci. USA, 99:14236 (2002); Byrom et al., Ambion TechNotes, 10(1):4-6(2003); Kawasaki et al., Nucleic Acids Res., 31:981-987 (2003); Knightet al.. Science, 293:2269-2271 (2001); and Robertson et al., J. Biol.Chem., 243:82 (1968)). Preferably, dsRNA are at least 50 nucleotides toabout 100, 200, 300, 400, or 500 nucleotides in length. A dsRNA may beas long as 1000, 1500, 2000, 5000 nucleotides in length, or longer. ThedsRNA can encode for an entire gene transcript or a partial genetranscript. In certain instances, siRNA may be encoded by a plasmid(e.g., transcribed as sequences that automatically fold into duplexeswith hairpin loops). A small hairpin RNA or short hairpin RNA (shRNA) isa sequence of RNA that makes a tight hairpin turn that can be used tosilence gene expression via RNA interference. The shRNA hairpinstructure is cleaved by the cellular machinery into siRNA, which is thenbound to the RNA-induced silencing complex (RISC). This complex binds toand cleaves mRNAs which match the siRNA that is bound to it. Suitablelength of the interference RNA are about 5 to about 200 nucleotides, or10-50 nucleotides or base pairs or 15-30 nucleotides or base pairs. Insome embodiments, the interference RNA is substantially complementary(such as at least about 60%, 70%, 80%, 90%, 95%, 98%, 99%, or moreidentical to) the corresponding target gene. In some embodiments, theinterference RNA is modified, for example by incorporating non-naturallyoccurring nucleotides. In some embodiments the targets and correspondingsequences are indicated below:

Target siRNA sense sequence Adenosine receptor5′-GCUGAAGCAGAUGGAGAGCCA-3′ A2A Adenosine receptor5′-GCUACACUUUUCACAAAAUUA-3′ A2B Angiotensin receptor5′-ATTGTCCCAAAGCTGGAAGGC-3′ 1 Angiotensin receptor5′-UUGAUAGGUACCAAUCUGUCA-3′ 2 Arrestin beta 15′-AUUACCAUGGAGAACCCAUCA-3′ Beta-catenin 5′-CGGGAUGUUCACAACCGAAUU-3′CCL2 5′-AUUAAUACAAAGAAUUUUUUU-3′ CCN1 5′-GUUACCAAUGACAACCUGAG-3′ CTGF5′-CCGGAGACAAUGACAUCUUUG-3′ OR 5′-GCACCAGUGUGAAGACAUA-3′ HSP475′-ACGAGAAGGAAAAGCUGCAAA-3′ LOXL2 5′-ACCAAAGUGUACAAAAUGUUU-3′ MMP25′-UUGAUGCGGUAUACGAGGCCC-3′ MMP9 5′-GGCGACCUCAAGUGGCACCAC-3′ PAI-15′-AGUUCAACUAUACUGAGUUCA-3′ PARP-1 5′-AUAACCGAAGAUUGCUGUGGC-3′ PDCD45′-AUAGAGAGAUGACAUCUAAGC-3′ PTEN 5′-UGUAAUGAUAUGUGCAUAUUU-3′ Smad 35′-UGUUCCAGUGUGUCUUAGAGA-3′ Smad 4 5′-GUUACUGUUGAUGGAUACGUG-3′ Smad 75′-CACUUCAAACUACUUUGCUGC-3′ SOX9 5′-AGAGAGGACCAACCAGAAUUC-3′ SPARC5′-AACAAGACCUUCGACUCUUCCC-3′ OR 5′-GCACCACACGUUUCUUUG-3′ STAT5A5′-GUUGUGAGUUUAGUAAGGCUG-3′ TGF beta receptor 15′-CUAUGCAAUGGGCUUAGUAUU-3′ TGF beta receptor 25′-AAUGACGAGAACAUAACACUA-3′ TGF beta receptor 35′-UAACAAUUGAUAUAAGACCUU-3′ TGF beta 1 5′-UUAAAAGUGGAGCAGCACGUG-3′Thrombospondin 1 5′-GCACGUGGUGUCUGUGGAAGA-3′ TIMP_15′-AAGGGUUCCAAGCCUUAGGGG-3′ TIMP-3 5′-CUGCAAGAUCAAGUCCUGCUA-3′ VEGF5′-AUGUGAAUGCAGAUGUGACAA-3′

In some embodiments, the nucleic acids are double-stranded antisenseRNA. Suitable length of the interference RNA are about 5 to about 200nucleotides, or 10-50 nucleotides or base pairs or 15-30 nucleotides orbase pairs. In some embodiments, the interference RNA is substantiallycomplementary (such as at least about 60%, 70%, 80%, 90%, 95%, 98%, 99%,or more identical to) the corresponding target gene. In someembodiments, the antisense RNA is modified, for example by incorporatingnon-naturally occurring nucleotides.

In some embodiments, the nucleic acids are miRNA. A microRNA(abbreviated miRNA) is a short ribonucleic acid (RNA) molecule found ineukaryotic cells. A microRNA molecule has very few nucleotides (anaverage of 22) compared with other RNAs. miRNAs are post-transcriptionalregulators that bind to complementary sequences on target messenger RNAtranscripts (mRNAs), usually resulting in translational repression ortarget degradation and gene silencing. The human genome may encode over1000 miRNAs, which may target about 60% of mammalian genes and areabundant in many human cell types. Suitable length of the miRNAs areabout 5 to about 200 nucleotides, or 10-50 nucleotides or base pairs or15-30 nucleotides or base pairs. In some embodiments, the miRNA issubstantially complementary (such as at least about 60%, 70%, 80%, 90%,95%, 98%, 99%, or more identical to) the corresponding target gene. Insome embodiments, the antisense RNA is modified, for example byincorporating non-naturally occurring nucleotides.

In some embodiments, the nucleic acids are plasmid DNA or DNA fragments(for example DNA fragments of lengths of up to about 1000 bp). Inaddition, the plasmid DNA or DNA fragments may be hypermethylated orhypomethylated.

Carrier molecules: The active agents described herein in someembodiments are associated with carrier molecules. Carrier molecules insome embodiments can be selected from the group consisting of a peptide,a protein, an antibody, a lipid, a phospholipid, a polymer, polycationicpolymers, an aptamer, a nanoparticle, a liposome, a dendrimer, apolymerosome, a viral vector, or a micelle. The carrier molecules can becombined with the desired active agents of interest to be delivered. Thecombinations may include covalent or non-covalent interactions betweenthe carriers and the active agents.

In some embodiments, the carrier molecule is a peptide, such as a cellpenetrating peptide. “Cell-penetrating peptide” as used herein refers toshort peptides that facilitate cellular uptake of various molecularcargo (from nanosize particles to small chemical molecules and largefragments of DNA). The “cargo” is associated with the peptides eitherthrough chemical linkage via covalent bonds or through non-covalentinteractions. The function of the CPPs are to deliver the cargo intocells, a process that commonly occurs through endocytosis with the cargodelivered to the endosomes of living mammalian cells. CPPs typicallyhave an amino acid composition that either contains a high relativeabundance of positively charged amino acids such as lysine or arginineor has sequences that contain an alternating pattern of polar/chargedamino acids and non-polar, hydrophobic amino acids. These two types ofstructures are referred to as polycationic or amphipathic, respectively.In some embodiments, the cell-penetrating peptide and the active agentsare combined to form complexes or nanoparticles.

Suitable cell-penetrating peptides include those disclosed in U.S. Pat.No. 7,906,484 and its counterparts, the contents of which are includedherein by reference in their entirety. Peptides of interest are thoseidentified by the formula GLFXALLXLLXSLWXLLLXAZ₁Z₂Z₃Z₄ wherein each X isindependently E, R, A, I, L, F, P, W, V, N, C, Q, G, S, T or Y, andwherein each of Z₁, Z₂, Z₃, and Z₄, is independently H, K, R, or Q.Specific sequences include GLFRALLRLLRSLWRLLLRAHHHH andGLFRALLRLLRSLWRLLLRARRRR. Other peptides of interest are thoseidentified in U.S. Pat. No. 6,841,535, U.S. Pat. No. 7,514,530, U.S.Pat. No. 7,579,318, U.S. Pat. No. 7,943,581, in Deshayes et al (2012),Small, DOI: 10.1002/smll.201102413, and in Rydstrom et al. (2011), PLoSONE 6(10): e25924. doi:10.1371/journal.pone.0025924, the contents ofwhich are included herein by reference in their entirety. Peptides ofinterest include for example the peptidesAc-GLWRALWRLLRSLWRLLWKA-cysteamide and corresponding modificationsincluding Ac-XLWRALWRLXRSLWRLLWKA-cysteamide [where X=G, L, beta-A, S,L, W, C or I], or Ac-XWRSXGWRWRXLWRWXXWXR-cysteamide [where X=L, S, G,beta-A, W, C or I]. In addition any of the peptides above can be stapledto improve their activity as is described by Zhang el al (2011) [[ZhangH, Curreli F, Zhang X, Bhattacharya S. Waheed A A. Cooper A, Cowburn D,Freed E O, Debnath A K. (2011) Antiviral activity of alpha-helicalstapled peptides designed from the HIV-1 capsid dimerization domain.Retrovirology. 2011 May 3; 8:28.]], the contents of which areincorporated herein by reference in their entirety.

Additional cell-penetrating peptides suitable for invention use aredisclosed in WO 2012/137150 A2 and WO 2012/137036 A1 both of which areincorporated by reference herein in their entirety. These includepeptides designated as the VEPEP-6 series and stapled peptidesdesignated as the ST-VEPEP-6 series and modifications thereof.

In the case of lipid based carriers, these are described in U.S. Pat.No. 8,058,069 or U.S. Pat. No. 8,034,376, the contents of which areincorporated herein by reference in their entirety. The term “lipid”refers to a group of organic compounds that include, but are not limitedto, esters of fatty acids and are characterized by being insoluble inwater, but soluble in many organic solvents. They are usually dividedinto at least three classes: (1) “simple lipids,” which include fats andoils as well as waxes; (2) “compound lipids,” which includephospholipids and glycolipids; and (3) “derived lipids” such assteroids. A “lipid particle” is used herein to refer to a lipidformulation that can be used to deliver an active agent or therapeuticagent, such as a nucleic acid (e.g., an interfering RNA), to a targetsite of interest. In the lipid particle of the invention, which istypically formed from a cationic lipid, a non-cationic lipid, and aconjugated lipid that prevents aggregation of the particle, the activeagent or therapeutic agent may be encapsulated in the lipid, therebyprotecting the agent from enzymatic degradation. As used herein, theterm “SNALP” refers to a stable nucleic acid-lipid particle. A SNALPrepresents a particle made from lipids (e.g., a cationic lipid, anon-cationic lipid, and a conjugated lipid that prevents aggregation ofthe particle), wherein the nucleic acid (e.g., siRNA, aiRNA, miRNA,ssDNA, dsDNA, ssRNA, short hairpin RNA (shRNA), dsRNA, or a plasmid,including piasmids from which an interfering RNA is transcribed) isfully encapsulated within the lipid. As used herein, the term “SNALP”includes an SPLP, which is the term used to refer to a nucleicacid-lipid particle comprising a nucleic acid (e.g., a plasmid)encapsulated within the lipid. SNALP and SPLP typically contain acationic lipid, a non-cationic lipid, and a lipid conjugate (e.g., aPEG-lipid conjugate). SNALP and SPLP are extremely useful for systemicapplications, as they can exhibit extended circulation lifetimesfollowing intravenous (i.v.) injection, they can accumulate at distalsites (e.g., sites physically separated from the administration site),and they can mediate expression of the transfected gene or silencing oftarget gene expression at these distal sites. SPLP include “pSPLP,”which comprise an encapsulated condensing agent-nucleic acid complex asset forth in PCT Publication No. WO 00/03683, the disclosure of which isherein incorporated by reference in its entirety for all purposes.

Other suitable carriers include ones such as ECHO (Wang et al, 2009,MOLECULAR PHARMACEUTICS VOL. 6, NO. 3, 738-746) and their modifications.EHCO (1-aminoethyl)iminobis[N-(oleicylcysteinylhistinyl-1-aminoethyl)propionamide], showspH sensitive amphiphilic cell membrane disruption. EHCO forms stablenanoparticles with siRNA. Targeted siRNA delivery systems are readilyformed by surface modification of the nanoparticles. PEGylation of thesiRNA/EHCO nanoparticles significantly reduces nonspecific cell uptake.The incorporation of a bombesin peptide or RGD peptide via a PEG spacerresults in receptor mediated cellular uptake and high gene silencingefficiency in U87 cells. Fluorescence confocal microscopic studiesdemonstrate that EHCO/siRNA nanoparticles and PEG modified EHCO/siRNAnanoparticles are able to facilitate endosomal escape of the siRNAdelivery systems. Systemic administration of a therapeutic anti-HIF-1RsiRNA with the peptide-targeted delivery systems results in significanttumor growth inhibition than a nontargeted delivery system or free siRNAvia intravenous injection in nude mice bearing human glioma U87xenografts. Modifications of ECHO are also useful for this purpose.

Pharmaceutical compositions: Preferred compositions of the presentinvention have more than one nucleic acid based active agent. In casewhere 2 active agents are used, they are present in molar ratios ofabout 1:9 to 9:1, more preferably in the range of about 3:7 to about7:3, and 4:6 to about 6:4 and most preferably at a ratio of 1:1. In thecase where 3 active agents are used, the preferred ranges of each activeagent are in the molar proportion of 1:1:8 to 8:1:1, or in the range of2:2:6 to 6:2:2, or in the range of 3:3:4 to 4:3:3 or present in equalproportions. In the case where more 4 active agents are used, it ispreferred to use them in the range of molar proportion of 1:1:1:7 to7:1:1:1, or in the range of 2:2:2:4 to 4:2:2:2 or have them present inequal proportions. When more than 4 active agents are used, it ispreferred to have them present in equal molar proportions.

The peptide-based particles of the invention typically have a meandiameter of from about 10 nm to about 300 nm, from about 50 nm to about200 nm, from about 60 nm to about 150 nm, from about 70 nm to about 110nm, or from about 70 to about 90 nm, and are substantially non-toxic.

Preferably, the molar ratio (peptide):(nucleic acid) in the complex isbetween 1:100 and 100:1, more preferably between 1:1 and 80:1, yet morepreferably between 5:1 and 30:1, most preferably between 8:1 and 20:1,and specifically 10:1, 15:1 or 20:1. The optimal molar ratio is easilydetermined by the skilled person, for example as described herein below.Specifically, the skilled person can test the transfection efficiency ofcomplexes having a variety of molar ratios (peptide):(nucieic acid) forany given peptide/nucleic acid combination, and will chose the ratiogiving the best transfection efficiency.

The lipid particles of the invention (e.g., SNALP) typically have a meandiameter of from about 40 nm to about 150 nm, from about 50 nm to about150 nm, from about 60 nm to about 130 nm, from about 70 nm to about 110nm, or from about 70 to about 90 nm, and are substantially non-toxic. Inaddition, nucleic acids, when present in the lipid particles of theinvention, are resistant in aqueous solution to degradation with anuclease. Nucleic acid-lipid particles and their method of preparationare disclosed in, e.g., U.S. Patent Publication Nos. 20040142025 and20070042031, U.S. Pat. No. 8,034,376, the disclosures of which areherein incorporated by reference in their entirety for all purposes.

Targeting: According to a particular embodiment, the complex of theinvention further comprise at least one iigand capable of cell-specificand/or nuclear targeting. A cell membrane surface receptor is a moleculeor structure which can bind said ligand with high affinity andpreferably with high specificity. Said cell membrane surface receptor ispreferably specific for a particular cell, i.e. it is foundpredominantly in one type of cell rather than in another type of cell(e.g. galactosyl residues to target the asialoglycoprotein receptor onthe surface of hepatocytes). The cell membrane surface receptorfacilitates cell targeting and internalization into the target cell ofthe ligand (i.e. the peptide involved in cell-specific targeting) andattached molecules (i.e. the complex of the invention). A large numberof ligand moieties/ligand binding partners that may be used in thecontext of the present invention are widely described in the literature.Such a ligand moiety is capable of conferring to the complex of theinvention, the ability to bind to a given binding-partner molecule or aclass of binding-partner molecules localized at the surface of at leastone target cell. Suitable binding-partner molecules include withoutlimitation polypeptides selected from the group consisting ofcell-specific markers, tissue-specific markers, cellular receptors,viral antigens, antigenic epitopes and tumor-associated markers.Binding-partner molecules may moreover consist of or comprise one ormore sugar, lipid, glycobpid or antibody molecules. According to theinvention, a ligand moiety may be for example a lipid, a glycol ipid, ahormone, a sugar, a polymer (e.g. PEG, polylysine, PEI), anoligonucleotide, a vitamin, an antigen, all or part of a lectin, all orpart of a polypeptide such as for example JTS1 (WO 94/40958), anantibody or a fragment thereof, or a combination thereof. Preferably,the ligand moiety used in the present invention is a peptide orpolypeptide having a minimal length of 7 amino acids. It is either anative polypeptide or a polypeptide derived from a native polypeptide.“Derived” means containing (a) one or more modifications with respect tothe native sequence (e.g. addition, deletion and/or substitution of oneor more residues), (b) ammo acid analogs, including not naturallyoccurring amino acids or (c) substituted linkages or (d) othermodifications known in the art. The polypeptides serving as ligandmoiety encompass variant and chimeric polypeptides obtained by fusingsequences of various origins, such as for example a humanized antibodywhich combines the variable region of a mouse antibody and the constantregion of a human immunoglobulin. In addition, such polypeptides mayhave a linear or cyclized structure (e.g. by flanking at bothextremities a polypeptide ligand by cysteine residues). Additionally,the polypeptide in use as ligand moiety may include modifications of itsoriginal structure by way of substitution or addition of chemicalmoieties (e.g. glycosylation, alkylation, acetylation, amidation,phosphorylation, addition of sulfhydryl groups and the like). Theinvention further contemplates modifications that render the ligandmoiety detectable. For this purpose, modifications with a detectablemoiety can be envisaged (i.e. a scintigraphic, radioactive, orfluorescent moiety, or a dye label and the like). Suitable radioactivelabels include but are not limited to .sup.99Tc, .sup.123I, and.sup.111In. Such detectable labels may be attached to the ligand moietyby any conventional techniques and may be used for diagnostic purposes(e.g. imaging of tumoral cells). In one special embodiment, thebinding-partner molecule is an antigen (e.g. a target cell-specificantigen, a disease-specific antigen, an antigen specifically expressedon the surface of engineered target cells) and the ligand moiety is anantibody, a fragment or a minimal recognition, unit thereof (i.e. afragment still presenting an antigenic specificity) such as thosedescribed in detail in immunology manuals (see for example Immunology,third edition 1993, Roitt, Brostoff and Male, ed Gambli, Mosby). Theligand moiety may be a monoclonal antibody. Monoclonal antibodies whichwill bind to many of these antigens are already known but in any case,with today's techniques in relation to monoclonal antibody technology,antibodies may be prepared to most antigens. The ligand moiety may be apart of an antibody (for eample a Fab fragment) or a synthetic antibodyfragment (for example, ScFv). According to an advantageous embodiment,the ligand moiety is selected among antibody fragments, rather thanwhole antibodies. Effective functions of whole antibodies, such ascomplement binding, are removed. ScFv and dAb antibody fragments may beexpressed as a fusion with one or more other polypeptides. Minimalrecognition units may be derived from the sequence of one or more of thecomplementary-determining regions (CDR) of the Fv fragment. Wholeantibodies, and F(ab′)2 fragments are “bivalent”. By “bivalent” we meanthat said antibodies and F(ab′) 2 fragments have two antigen bindingsites. In contrast, Fab, Fv, ScFv, dAb fragments and minimal recognitionunits are monovalent, having only one antigen binding sites. In apreferred embodiment, the ligand moiety allows to target a tumor celland is capable of recognizing and binding to a molecule related to thetumor status, such as a tumor-specific antigen, a cellular proteindifferentially or over-expressed in tumor cells or a gene product of acancer-associated virus. Examples of tumor-specific antigens include butare not limited to MUC-1 related to breast cancer (Hareuveni et al.,1990, Eur. J. Biochem 189, 475-486), the products encoded by the mutatedBRCA1 and BRCA2 genes related to breast and ovarian cancers (Miki etal., 1994, Science 226, 66-71; Futreal et al., 1994, Science 226,120-122; Wooster et al., 1995, Nature 378, 789-792), ARC related tocolon cancer (Polakis, 1995, Curr. Opin. Genet. Dev. 5, 66-71), prostatespecific antigen (PSA) related to prostate cancer, (Stamey et al., 1987,New England J. Med. 317, 909), carcinoma embryonic antigen (CEA) relatedto colon cancers (Schrewe et al., 1990, Mol. Cell. Biol, 10, 2738-2748),tyrosinase related to melanomas (Vile et al., 1993, Cancer Res. 53,3860-3864), receptor for rnelanocyte-stimulatlng hormone (MSH) which isexpressed in high number in melanoma cells, ErbB-2related to breast andpancreas cancers (Harris et al, 1994, Gene Therapy 1, 170-175), andalpha-foctoprotein related to liver cancers (Kanai et al., 1997, CancerRes, 57, 461-465). A special ligand moiety in use in the presentinvention is a fragment of an antibody capable of recognizing andbinding to the MUC-1 antigen and thus targeting the MUC-1 positive tumorcells. A more preferred ligand moiety is the scFv fragment of the SM3monoclonal antibody which recognizes the tandem repeat region of theMUC-1 antigen (Burshell et al., 1987, Cancer Res. 47, 5476-5482; Girlinget al., 1989, Int J. Cancer 43, 1072-1076; Dokurno et al., 1998, J. Mol.Biol. 284, 713-728). Examples of cellular proteins differentially oroverexpressed in rumor cells include but are not limited to the receptorfor interleukin 2 (IL-2) overexpressed in some lymphoid tumors, GRP(Gastrin Release Peptide) overexpressed in lung carcinoma cells,pancreas, prostate and stomach tumors (Michael et al., 1995, GeneTherapy 2, 660-668), TNF (Tumor Necrosis Factor) receptor, epidermalgrowth factor receptors. Fas receptor, CD40 receptor, CD30 receptor,CD27 receptor, OX-40, .alpha.-v integrins (Brooks et al., 1994, Science264, 569) and receptors for certain angiogenic growth factors (Hanahan,1997, Science 277, 48). Based on these indications, it is within thescope of those skilled in the art to define an appropriate ligand moietycapable of recognizing and binding to such proteins. To illustrate, IL-2is a suitable ligand moiety to bind to IL-2 receptor. In the case ofreceptors that are specific to fibrosis and inflammation, these includethe TGFbeta receptors or the Adenosine receptors that are identifiedabove and are suitable targets for invention compositions. The presentapplication also provided methods of making any one of the compositionsdescribed herein. For example, the method of making a pharmaceuticalcomposition comprising nanoparticles comprising a cell penetratingpeptide and two or more active agents generally involve the followingsteps. Peptide-siRNA nanoparticles with multiple siRNA combinations areprepared by mixing amphipathic peptide and the desired individualsiRNAs. Stock solutions of amphipathic peptide are prepared at 1 mg/mL(0.1-10 mg/ml range) in distilled water and sonicated for 10 min. Stocksolutions of the multiple siRNA together are prepared at 100 μM (10-200uM range), total concentrations in 50 mM Tris, 0.5 mM EDTA buffer.Peptide/siRNA complexes containing multiple siRNA, are taken in equalproportions (or any desired proportion) and are formed in pure water byincubating peptide (373 μM stock solution (range 50-500 uM)) with thesiRNA mixture for 30 min (range 1 minute-60 minutes) at 37 C (rangerefrigerated to 50 C) with final molar ratio of peptide and siRNA at20:1 (range 1:1 to 100:1). Alternately, the core complex may be formedfirst at a peptide to siRNA ratio of about 5:1 (range 0.1:1 to 10:1)followed by a second step of incubation of the peptide with the corecomplex at a ratio of 20:1 (range 1:1 to 100:1). Peptide-siRNAnanoparticles can be further characterized for physieochemicalproperties in vitro for key parameters including particle size, surfacecharge, particle stability in suspension and in plasma, and siRNAintegrity in plasma. In addition, these particles may be lyophilizedwith addition of suitable excipients such as sugars or proteins such asalbumin.

III. Methods of the Present Invention

The pharmaceutical compositions described herein are useful for treatingfibrosis and/or inflammatory conditions. In some embodiments, thecompositions are useful for reducing fibrous conncctive tissues in anindividual having fibrosis. In some embodiments, the compositions areuseful for inhibiting inflammation in an individual. These compositionscan reduce fibrosis as indicated by a reduction in collagen in therelevant tissues, such as in lungs, skin, liver etc. In addition,markers of fibrosis and relevant fibrosis and inflammation related genesor gene products such as SPARC, CTGF, TGF beta receptors, TIMPs, etc.may be directly measure in relevant tissues as an indication ofeffectiveness. Functional endpoints in patients, in particular inpatients with Idiopathic pulmonary fibrosis which are indicators of lungfunction such a mean 6 minute walking distance, blood oxygenationlevels, etc. are also relevant indicators of the effectiveness oftherapy. The compositions described herein can therefore be useful forany one or more of the following: 1) inhibiting fibrosis; 2) inhibitinginflammation; 3) reducing the amount of collagen; 4) inhibiting (such assimultaneously inhibiting) expression of two or more target genes (suchas target genes described herein); 5) increasing functional walkingdistance; and 6) improving quality of life.

Different diseases to be treated: The present invention comprisespharmaceutical compositions to treat fibrosis or inflammatory conditionsor diseases, including but not limited to: pulmonary fibrosis,idiopathic pulmonary fibrosis, progressive massive fibrosis of the lung,cystic fibrosis, mediastinal fibrosis, liver fibrosis, cirrhosis,endomyocardial fibrosis, cardiac fibrosis, old myocardial infarction,progressive kidney disease, renal fibrosis, myelofibrosis,retroperitoneal fibrosis, nephrogenic systemic fibrosis, Crohn'sdisease, keloids, scleroderma/systemic sclerosis, arthrofibrosis,adhesive capsulitis, fibromyalgia, peritoneal fibrosis, radiationinduced fibrosis, burn induced fibrosis, trauma induced fibrosis,scarring fibrosis, and wound healing fibrosis. The inventioncompositions are also useful for wound healing resulting from traumaticinjury such as bums or for healing of chronic wounds and reducingscarring and fibrosis.

The present invention comprises pharmaceutical compositions to treatdesmoplastic cancers or cancers having a flbrotic component, includingbut not limited to: squamous cell carcinomas independent of theirlocation, bilio-panereaiic carcinomas, mesothelioma, desmoplasticfibroma, desmoplastic round cell tumor, breast cancer, ovarian cancer,colorectal carcinoma and tumors of gastrointestinal tract, lung cancers,lymphomas, myelofibrosis, leukemias melanoma, brain tumors (includingglioblastoma, cerebral astrocytoma, neuroblastoma, and medulloblastoma),bladder cancers, hepatocellular and urothelial tumors, and tumors of thepituitary gland.

Diseases: Idiopathic pulmonary fibrosis (IPF): IPF is a progressive andgenerally fatal disease characterized by scarring of the lungs thatthickens the lung lining, causing an irreversible loss of lung structureand function. IPF affects 5 million people worldwide and 130,000-200,000people in the US, with about 48,000 new cases diagnosed and 40,000deaths each year, with medical costs estimated at $2.8 billion per100,000 patients [2, 3]. Median survival is 2-4 years followingdiagnosis, and the 5-year survival is 20-40% [4, 5]. Currently, there isno known cause, no FDA approved treatments and no cure for IPF [6]. IPFpatients typically are treated with anti-inflammatory drugs, includingcorticosteroids and cytotoxic agents, despite the fact that there is noevidence that they have any effect on long-term patient survival.

Systemic Scleroderma (SS): SS is an autoimmune disorder and a connectivetissue disease that involves changes in the skin, blood vessels,muscles, and internal organs. There are an estimated 300,000 people inthe US who have scleroderma, a third of whom have SS [7]. Local diseaseaffects only skin tissues while SS affects skin and underlying tissues,blood vessels, and major organs including the heart, lungs, or kidneys.In diffuse cutaneous disease, five-year survival is 70%, and 10-yearsurvival is 55% [8]. Currently there is no cure and no specifictreatment for scleroderma. SS treatment includes immunosuppressive andanti-inflammatory drugs including corticosteroids, methotrexate,cyclophosphamide, azathioprine, and mycophenolate [9, 10].

Liver cirrhosis (LC): Liver fibrogenesis is characterized by excessiveaccumulation of extra-cellular matrix (ECM), leading to cirrhosis andcomplications including portal hypertension, liver failure, andhepatocellular carcinoma [11]. LC causes 800,000 deaths worldwideannually [12]. In the US, LC causes 27,000 deaths annually [13].Established cirrhosis has a 10-year mortality of 34-66% [14]. Commoncauses of cirrhosis include alcohol consumption, chronic hepatitis B, Cand D, obesity, toxins, bile duct diseases, and autoimmune hepatitis[15]. Currently there is no treatment available for LC, and health carecosts for managing this disease are high.

Pancreatic cancer and some other cancers are known to have a fibrotic ordesmoplastic stroma. However there have been no studies to specificallytarget the stromal components of pancreatic cancer. Peptide basednanopanicles containing siRNA targeted to CTGF, SPARC, ITMPs, TGFbetaior 2, MMPs and beta-catenin are of particular interest for pancreaticcancer.

Patient selection based on gene and protein expression profiling:Standard techniques of gene expression profiling, histology,immunohistochemistry, proteomic analysis, and other well acceptedtechniques for determining the level of DNA, mRNA, proteins and otherbiomarkers in patient samples can be utilized to identify the genes orproteins that axe of particular interest in treating the patient. Forexample, if a patient is detected to have a high level expression of aparticular gene or protein, then the pharmaceutical composition may beappropriately adjusted to match the particular condition of the patient.Thus, if the patient has a high level of CTGF or SPARC, thepharmaceutical composition to be administered to said patient maycontain appropriate amounts of active agents to suppress CTGF or SPARC.Based on this analysis a suitable pharmaceutical composition may beselected to selectively treat or inhibit particular genes or proteins toameliorate the pathological condition. Thus, for example, the presentapplication in some embodiments provides a method of treating a fibroticor inflammatory condition in an individual, comprising administering tothe individual an effective amount of a pharmaceutical compositioncomprising one or more active agents (such as nucleic acids, includingoligonucleotides for example interfering RNAs) that modulate theexpression of two or more genes involved in the development orprogression of fibrosis or inflammation, wherein the individual isselected based on the expression level of at least one genes involvedits the development and progression of fibrosis or inflammation. In someembodiments, the active agents are selected based on the expressionprofile to inhibit the expression of selected target genes.

In some embodiments, there is provided a method of treating a fibroticor inflammatory condition in an individual, comprising: 1) determiningthe expression level of at least one (including for example at leastabout any of 2, 3, 4, 5, 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, ormore) genes involved in the development and progression of fibrosis orinflammation, and 2) administering to the individual an effective amountof a pharmaceutical composition comprising one or more active agents(including nucleic acids, such as oligonucleotides for exampleinterfering RNAs) that modulate the expression of two or more genesinvolved in the development or progression of fibrosis or inflammation.In some embodiments, the active agents are selected based on theexpression profile to inhibit the expression of selected target genes.

Dosage, administration route: The pharmaceutical compositions may beadministered by oral, intravenous, intraarterial, intracardiac,intracatheter, intraperitoneal, intravesical, transdermal, nasalinhalation, pulmonary delivery, intracavity, intracranial, intrathecal,subcutaneous, intradermal, intramuscular, intraocular, topical, rectal,vaginal, direct injection/administration, or local delivery witheleetrotransfer or microneedle injection.

Dosages of the pharmaceutical compositions of the present inventionfound to be suitable for treatment of human or mammalian subjects are inthe range of 0.001 mg/kg-100 mg/kg of the active agent. More preferreddosage ranges are 0.1-20 mg/kg and more preferably in the range of0.5-10 mg/kg, e.g. 0,1-0.5, 0.5-1. The schedule of administration to thesubject may range from a single administration that constitutes theentire treatment to daily administration. More preferably, theadministration is once every 3-30 days and most preferably once every4-7 days.

IV. Kits, Compositions, Reagents, and Article of Manufacture

Also provided herein are kits, reagents, and articles of manufactureuseful for the methods described herein. Such kits may contain vialscontaining the carrier molecules separately from vials containing theactive agents. At the time of patient, treatment, it is first determinedwhat particular pathology is to be treated based on for example, geneexpression analysis or proteornie or histological analysis of patientsamples. Having obtained those results, the carrier molecules are mixedwith the appropriate active agent molecules to result In complexes ornanoparticies that can be administered to the patient for an effectivetreatment. Thus, in some embodiments, there is provided a kitcomprising: 1) two or more active agents (such as nucleic acids, forexample oligonucleotides); 2) a cell-penetrating peptide. In someembodiments, the kit further comprises agents for determining geneexpression profiles. In some embodiment, the kit further comprises apharmaceuticaliy acceptable carrier.

The kits described herein may further comprise instructions for usingthe components of the kit to practice the subject methods (for exampleinstructions for making the pharmaceutical compositions described hereinand/or for use of the pharmaceutical compositions). The instructions forpracticing the subject methods are generally recorded on a suitablerecording medium. For example, the instructions may be printed on asubstrate, such as paper or plastic, ctc. As such, the instructions maybe present in the kits as a package insert, in the labeling of thecontainer of the kits or components thereof (i.e., associated with thepackaging or sub packaging) etc. In some embodiments, the instructionsare present as an electronic storage data file present on a suitablecomputer readable storage medium, e.g., CD-ROM, diskette, etc. In yetother embodiments, the actual instructions are not present in the kit,but means for obtaining the instructions from a remote source, e.g., viathe internet, are provided. An example of this embodiment is a kit thatincludes a web address where the instructions can be viewed and/or fromwhich the instructions can be downloaded. As with the instructions, thismeans for obtaining the instructions is recorded on a suitablesubstrate.

The various components of the kit may be in separate containers, wherethe containers may be contained within a single housing, e.g., a box.

Further provided herein are methods of making any of the articles ofmanufacture described herein.

The invention is described in detail below and comprises:

A method of treating a fibrotic or inflammatory condition in anindividual, comprising administering to the individual an effectiveamount of a pharmaceutical composition comprising one or more nucleicacids that modulate the expression of two or more genes involved in thedevelopment or progression of fibrosis or inflammation.

In some embodiments, the two or more genes are selected from the groupconsisting of CTGF(CCN2), TGFbetai, TGFbeta receptor 1, TGFbeta receptor2, TGFbeta receptor 3, beta-catenin, SPARC, VEGF, Angiotensin II, TIMP,HSP47, thrombospondin, CCN1, LOXL2, MMP2, MMP9, CCL2, Adenosine receptorA2A, Adenosine receptor A2B, Adenylyl cyclase, Smad 3, Smad 4, Smad 7,SOX9, arrestin, PDCD4, PAI-1, NF-kB, and PARP-1 GAD65, sGAD65, BAX, p53PTEN, STAT5, smoothened, GLI1, GLI2, and Patched-1. Yet another gene ofinterest for the present invention is HIF-1alpha.

In some embodiments, there is provided a method of treating a fibroticor inflammatory condition in an individual, comprising administering tothe individual an effective amount of a pharmaceutical compositioncomprising one or more active agents that modulate the activity orexpression of two or more genes involved in the development andprogression of fibrosis or inflammation, selected from, CTGF(CCN2),TGFbetai, TGFbeta receptor 1, TGFbeta receptor 2, TGFbeta receptor 3,beta-catenin, SPARC, VEGF, Angiotensin II, TIMP, HSP47, thrombospondin,CCN1, LOXL2, MMP2, MMP9, CCL2, Adenosine receptor A2A, Adenosinereceptor A2R, Adenylyl cyclase, Smad 3, Smad 4, Smad 7, SOX9, arrestin,PDCD4, PAI-1, NF-kB. and PARP-1 GAD65, sGAD65, BAX, p53 PTEN, STAT5,smoothened, GLI1, GLI2, and Patched-1. Yet another gene of interest forthe present invention is MIF-1alpha.

In some embodiments, according to methods described above, the one orsnore active agents are nucleic acids.

In some embodiments, according to methods described above, at least oneof the nucleic acids is a single stranded oligonucleotide.

In some embodiments, according to methods described above, at least oneof the nucleic acids is a double stranded oligonucleotide.

7 In some embodiments, according to methods described above, at leastone of the nucleic acids is selected from the group consisting ofantisense oligonucleotide, RNAi, shRNA, siRNA, miRNA, or plasmid DNA.

In some embodiments, according to methods described above, at least oneof the nucleic acids is RNAi.

In some embodiments, according to methods described above, at least oneof the nucleic acids is siRNA.

In some embodiments, according to methods described above, the at leastone of the nucleic acids is shRNA.

In some embodiments, according to methods described above, at least oneof the nucleic acids is about 10 to about 50 nucleotides long.

In some embodiments, according to methods described above, thecomposition comprises two or more nucleic acids.

In some embodiments, according to methods described above, the two ormore nucleic acids are of the same kind.

In some embodiments, according to methods described above, the two ormore nucleic acids are of different kinds.

In some embodiments, according to methods described above, thecomposition comprises two nucleic acids, and wherein the molar ratio ofthe two nucleic acids is about 0.1:1 to about 10:1.

In some embodiments, according to methods described above, the two ormore nucleic acids in the pharmaceutical composition are in equal molarproportions.

In some embodiments, according to methods described above, the nucleicacids are associated with a carrier molecule.

In some embodiments, according to methods described above, the nucleicacids are covalcntly associated with the carrier molecule.

In some embodiments, according to methods described above, the nucleicacids are non-covalently associated with the carrier molecule

In some embodiments, according to methods described above, the carriermolecule is selected from the group consisting of a peptide, a protein,an antibody, a lipid, a phospholipid, a polymer, an aptamer, ananoparlicle, a liposome, a dendrimer, a polymerosome, a viral vector,and a micelle.

In some embodiments, according to methods described above, the earnermolecule is a peptide.

In some embodiments, according to methods described above, the peptideis a cell-penetrating peptide.

In some embodiments, according to methods described above, thecell-penetrating peptide is selected from the group consisting of aPTD-based peptide, an amphipathic peptide, a poly-arginine-basedpeptide, a MPG peptide, a CADY peptide, Pep-1 peptide or a Pep-2peptide.

In some embodiments, according to methods described above, the nucleicacids and the cell-penetrating peptide are present in a complex.

In some embodiments, according to methods described above, thecomposition comprises nanoparticles comprising the complexes of thenucleic acids and the cell-penetrating peptide.

In some embodiments, according to methods described above, the averagesize of the nanoparticies is between 50 and 400 nm.

In some embodiments, according to methods described above, the molarratio of the cell-penetrating peptide and the nucleic acids in thecomposition is about 100:1 to about 1:50.

In some embodiments, according to methods described above, the activeagents modulate the activity or expression of two or more genes selectedfrom: SPARC, CTGF, TGFbetai, TGFbeta receptor 1, TGFbeta receptor 2,TGFbeta receptor 3, beta-catenin, Adenosine receptor A2A, Adenosinereceptor A2B, TIMPs.

In some embodiments, according to methods described above, the activeagents modulate the activity of SPARC and TGFbeta1.

In some embodiments, according to methods described above, the fibroticor inflammatory condition is selected from the group consisting ofpulmonary fibrosis, idiopathic pulmonary fibrosis, progressive massivefibrosis of the lung, cystic fibrosis, mediastinal fibrosis, liverfibrosis, cirrhosis, endomyocardial fibrosis, cardiac fibrosis, oldmyocardial infarction, progressive kidney disease, renal fibrosis,myelofibrosis, retroperitoneal fibrosis, nephrogenic systemic fibrosis,Crohn's disease, keloids, scleroderma/systemic sclerosis,arthrofibrosis, adhesive capsulitis, fibromyalgia, peritoneal fibrosis,radiation induced fibrosis, burn induced fibrosis, trauma inducedfibrosis, scarring fibrosis, and wound healing fibrosis.

In some embodiments, according to methods described above, the fibroticor inflammatory conditions is a desmoplastic cancer, wherein thedesmoplastic cancer is selected from the group consisting of: squamouscell carcinoma independent of their location, bilio-pancreaticcarcinoma, mesothelioma, desmoplastic fibroma, desmoplastic round celltumor, breast cancer, ovarian cancer, colorectal carcinoma and tumor ofgastrointestinal tract, lung cancer, lymphoma, myelofibrosis, leukemia,melanoma, brain tumor (including glioblastoma, cerebral astrocytoma,neuroblastoma, and medulloblastoma), bladder cancer, hepatocellular andurothelial tumor, and tumor of the pituitary gland.

In some embodiments, according to methods described above, saidpharmaceutical composition is administered by oral, intravenous,intraarterial, intracardiac, intracatheter, intraperitoneal,intravesical, transdermal, nasal inhalation, pulmonary delivery,intracavity, intracranial, intrathecal, subcutaneous, intradermal,intramuscular, intraocular, topical, rectal, vaginal, directinjection/administration, or local delivery with electrotransfer ormicroneedle injection.

In some embodiments, according to methods described above, theindividual is selected based on the expression level of at least onegenes involved in the development and progression of fibrosis orinflammation.

In some embodiments, according to methods described above, the inventionrequires further determining the expression level of at least one geneprior to the administration of the pharmaceutical composition.

In some embodiments, the invention comprises a pharmaceuticalcomposition comprising two or more active agents that modulate theexpression of two or more genes involved in the development orprogression of fibrosis or inflammation.

In some embodiments, the invention requires that the two or more genesare selected from the group consisting of CTGF(CCN2), TGPbetai, TGFbetareceptor 1, TGFbeta receptor 2, TGFbeta receptor 3, beta-catenin, SPARC,VEGF, Angiotensin II, TIMP, HSP47, thrombospondin, CCN1, LOXL2, MMP2,MMP9, CCL2, Adenosine receptor A2A, Adenosine receptor A2B, Adenylylcyclase, Smad 3, Smad 4, Smad 7, SOX9, arrestin, PDCD4, PAI-1, NF-kB,and PARP-1 GAD65, sGAD65, BAX, p53 PTEN, STAT5, smoothened, GLI1, GLI2,and Patched-1. Yet another gene of interest for the present invention isHIF-1alpha.

In some embodiments, the invention requires that the two or more activeagents are of the same kind.

In some embodiments, the invention requ ires that the two or more activeagents are of different kinds.

In some embodiments, the invention requires that the compositioncomprises two active agents, and wherein the molar ratio of the twoactive agents is about 0.1:1 to about 10:1.

In some embodiments, the invention requires that the two or more activeagents in the pharmaceutical composition are in equal molar proportions.

In some embodiments, the invention requires that the two or more activeagents are nucleic acids.

In some embodiments, the invention requires that at least one of thenucleic acids is a single stranded oligonucleotide.

In some embodiments, the invention requires that at least one of thenucleic acids is a double stranded oligonucleotide.

In some embodiments, tire invention requires that at least one of thenucleic acids is selected from the group consisting of antisenseoligonucleotide, RNAi, shRNA, siRNA, miRNA, or plasmid DNA.

In some embodiments, the invention requires that at least one of thenucleic acids is RNAi.

In some embodiments, the invention requires that at least one of thenucleic acids is siRNA.

In some embodiments, the invention requires that at least one of thenucleic acids is shRNA.

In some embodiments, the invention requires that at least one of thenucleic acids is about 10 to about 50 nucleotides long.

In some embodiments, the invention requires that the nucleic acids areassociated with a carrier molecule.

In some embodiments, the invention requires that the nucleic acids arecovalently associated with the carrier molecule.

In some embodiments, the invention requires that the nucleic acids arenon-covalently associated with the carrier molecule.

In some embodiments, the invention requires that the carrier molecule isselected from the group consisting of a peptide, a protein, an antibody,a lipid, a phospholipid, a polymer, an aptamer, a nanoparticie, aliposome, a dendrimer, a polymerosome, a viral vector, and a micelle.

In some embodiments, the invention requires that the carrier molecule isa peptide.

In some embodiments, the invention requires that the peptide is acell-penetrating peptide.

In some embodiments, the invention requires that the cell-penetratingpeptide is selected from the group consisting of a PTD-based peptide, anamphipathie peptide, a poly-arginine-based peptide, a MPG peptide, aCADY peptide, Pep-1 peptide, or a Pep-2 peptide.

In some embodiments, the invention requires that the nucleic acids andthe cell-penetrating peptide are present in a complex.

In some embodiments, the invention requires that the compositioncomprises nanoparticles comprising the complexes of the nucleic acidsand the cell-penetrating peptide.

In some embodiments, the invention requires that the average size of thenanoparticles is between 50 and 400 nm.

In some embodiments, the invention requires that the molar ratio of thecell-penetrating peptide and the nucleic acids in the composition isabout 100:1 to about 1:50.

EXAMPLES

The following are examples of methods and compositions of the invention.It is understood that various other embodiments may be practiced, giventhe general description provided above.

Example 1a

This example provides information on preparation of peptide-siRNAcomplexes. Preparation and characterization of peptide-siRNAnanoparticles: The siRNA sequences will be designed to target 8 selectedmouse genes: TGFbeta receptors 1 and 2, CTGF, adenosine receptors A2Aand A2B, SPARC, and TIMP-1 and -3. Peptide-siRNA nanoparticles areprepared by mixing amphipathic peptide and individual siRNAs targetingfibrosis-related genes. Stock solutions of amphipathic peptide areprepared at 1 mg/mL in distilled water and sonicated for 10 min. Stocksolutions of siRNA are prepared at 100 μM concentrations in 50 mM Tris,0.5 mM EDTA buffer. Peptide/siRNA complexes are formed in pure water byincubating peptide (373 μM stock solution) with siRNA (100 μM stocksolution) for 30 min at 37 C with final molar ratio of peptide and siRNAat 20:1. Peptide-siRNA nanoparticles will be characterized forpbysicochemical properties in vitro for key parameters includingparticle size, surface charge, particle stability in suspension and inplasma, and siRNA integrity in plasma.

Example 1b

This example provides information on preparation of peptide-multiplesiRNA complexes. Preparation and characterization of peptide-siRNAnanoparticles: The siRNA sequences will be designed to target 8 selectedmouse genes: TGFbeta receptors 1 and 2, CTGF, adenosine receptors A2Aand A2B, SPARC, and TIMP-1 and -3. Peptide-siRNA nanoparticles withmultiple siRNA combinations are prepared by mixing amphipathic peptideand the desired individual siRNAs targeting fibrosis-related genes.Stock solutions of amphipathic peptide are prepared at 1 mg/mL indistilled water and sonicated for 10 min. Stock solutions of themultiple siRNA together are prepared at 100 μM total concentrations in50 mM Tris, 0.5 mM EDTA buffer. Peptide/siRNA complexes containingmultiple siRNA, e.g., siRNA for SPARC, TGFbeta receptor 1 and adenosinereceptors A2A are taken in equal proportions and are formed in purewater by incubating peptide (373 μM stock solution) with the siRNAmixture (100 μM stock solution) for 30 min at 37 C with final molarratio of peptide and siRNA at 20:1. Alternately, the core complex may beformed first at a peptide to siRNA ratio of about 5:1 followed by asecond step of incubation of the peptide with the core complex at aratio of 20:1. Peptide-siRNA nanoparticles will be characterized forphysicochemical properties in vitro for key parameters includingparticle size, surface charge, particle stability in suspension and inplasma, and siRNA integrity in plasma.

Example 2

This example provides information to show that SPARC and CTGF siRNAreduce expression of collagen type 1 in skin fibroblasts of CTGFtransgenic mice. Transgenic mice that over-express connective tissuegrowth factor (CTGF) in fibroblasts under the control of anenhancer/promoter element of the Colla2 gene (Colla2-CTGF) recapitulatemultiorgan fibrosis similar to fibrosis observed in Scleroderma (SSc).In this study the regulation of Sparc and Ctgf siRNAs on the expressionof several extracellular matrix components in the fibroblasts derivedfrom Colla2-CTGf transgenic mice was investigated. Three fibroblastlines were obtained from each of wide type C57BL/6 and CTGF transgenicC57BL/6, and were transfected with either Sparc siRNA or Ctgf siRNA.Real-time quantitative RT-PCR and Western blotting were used to examinethe transcription and protein levels of type I collagen, CTGF and SPARC.Student's t-tests were used to determine the significance of theresults. The results showed that Colla2 and Ctgf increased expression atboth transcriptional and translational levels in the fibroblasts fromthe Colla2-CTGF transgenic mice compared with those in the fibroblastsfrom their normal wild-type littermate. The treatment with Sparc siRNAor Ctgf siRNA attenuated the mRNA and/or protein expression of theColla2, Ctgf and Sparc in these fibroblasts. Sparc and Ctgf siRNAs alsoshowed a reciprocal inhibition at transcript levels. Therefore, theresults indicated that both SPARC and CTGF independently appeared to beinvolved in the same biological pathway, and they have the potential toserve as a therapeutic target for fibrotic diseases such as SSc.

Example 3

This example provides information to show that SPARC and CTGF siRNAreduce bleomycin induced skin and lung fibrosis in mice. SPARC is amatricellular protein, which, along with other extracellular matrixcomponents including collagens, is commonly over-expressed in fibroticdiseases. The purpose of this study was to examine whether inhibition ofSPARC can regulate collagen expression in vitro and in vivo, andsubsequently attenuate fibrotic stimulation by bleomycin in mouse skinand lungs. In in vitro studies, skin fibroblasts obtained from a Tgfbr1knock-in mouse (TBRICA; Cre-ER) were transfected with SPARC siRNA. Geneand protein expressions of the Colla2 and the Ctgf were examined byreal-time RT-PCR and Western blotting, respectively. In in vivo studies,C57BL/6 mice were induced for skin and lung fibrosis by bleomycin andfollowed by SPARC siRNA treatment through subcutaneous injection andintratracheal instillation, respectively. The pathological changes ofskin and lungs were assessed by hematoxylin and eosin and Masson'strichrome stains. The expression changes of collagen in the tissues wereassessed by real-time RT-PCR and non-crosslinked fibrillar collagencontent assays. SPARC siRNA significantly reduced gene and proteinexpression of collagen type 1 in fibroblasts obtained from the TBRICA;Cre-ER mouse that was induced for constitutiveiy active TGF-betareceptor I. Skin and lung fibrosis induced by bleomycin was markedlyreduced by treatment with SPARC siRNA. The anti-fibrotic effect of SPARCsiRNA in vivo was accompanied by an inhibition of Ctgf expression inthese same tissues. Specific inhibition of SPARC effectively reducedfibrotic changes in vitro and in vivo. SPARC inhibition may represent apotential therapeutic approach to fibrotic diseases

Example 4

This example provides information to show the Vitro Evaluation ofPeptide-siRNA Nanoparticies.

The peptide-siRNA nanoparticies carrying individual siRNAs againstfibrogenic genes and their combinations will be evaluated in vitro incell culture of 3 different fibrosis models for the efficacy of siRNAdelivery into the cells, target down regulation, and the inhibition ofcollagen deposition. The effect of different siRNAs will be compared toidentify the interaction between multiple fibrogenic genes and pathwaysand rationally select optimal combinations for in vivo testing againstfibrosis mouse models. In vitro siRNA delivery by peptide-siRNAnanoparticles in cell cultures of 3 fibroblast models:

Cell culture: Three established in vitro cell lines of fibrosis areselected: CTGF overexpressing mouse fibroblasts isolated from CTGFtransgenic mice [21], TGFbeta rcccptor 1overexpressing mouse skinfibroblasts isolated with TGFbetaR1 knock-in mice [29], and mouse skinfibroblasts isolated from ADA-null mice [39].

In vitro siRNA delivery: Nanoparticies containing different siRNAs andtheir combinations and scrambled siRNA are incubated with mousefibroblasts for 30 minutes followed by fresh DMEM/10% FCS.

Collection and Processing of Samples: Seventy-two hours following siRNAdelivery, cells are harvested, followed by mRNA and proteinpurification.

Analysis: The mRNA and protein levels of target genes and collagen I areanalyzed by real time RT-PCR and western blot, respectively.

Outcomes: Levels of target and collagen I mRNA and proteins will becompared between control and the treated groups to determine the extentof gene knockdown and the effect on collagen deposition. Effective downregulation of key fibrogenic genes can abolish the collagen depositionshown in the in vitro fibrosis models. The effect of individual siRNAand combinations on different fibrogenic genes will be analyzed todetermine interactions between multiple fibrotic genes and signalingpathways and to identify potential synergistic interactions.

Example 5

This example provides information to show the In Vivo Screening and DoseRanging Study of Peptide-siRNA Nanoparticies

In vivo screening and dose ranging study will be conducted in bleomycinpulmonary and adenosine deaminase deficient (ADA-null) mouse models toidentify optimal siRNA combinations and dose. Different mouse fibrosismodels have distinct molecular pathology for disease progression.Therefore, 2 independent models of fibrosis are employed for in vivotesting of peptide-siRNA nanoparticies selected through in vitroscreening in Example 4. Pulmonary fibrosis model caused by intratracheal(IT) instillation of bleomycin was reported before [29]. ADA-null micelacking adenosine deaminase accumulate high levels of adenosine, whichresults in severe diffuse dermal fibrosis and premature deaths 3 weeksafter birth from pulmonary inflammation and fibrosis [40]. Testing ofselected peptide-siRNA nanoparticies at different dose levels willdetermine a safe and effective dose for target gene down regulation, aswell as provide preliminary indication on the anti-fibrogenic efficacyin vivo. The siRNA nanoparticies will be administered both intravenously(IV) and IT in the bleomycin pulmonary fibrosis model to compare thesafety and efficacy of systemic and local delivery. The ADA-null micewill be administered IV to test the ability for systemic therapy tocontrol a diffused systemic fibrotic disease. The key promoters offibrosis in different models can be identified and used to rationallydesign the most optimal siRNA combinations for in vivo efficacy testingin Example 5.

Mouse fibrosis models: Bleomycin-induced pulmonary fibrosis model willbe generated following established method by one-time IT instillation ofC57BL/6 mice with 3.5 units/kg bleomycin dissolved in saline [29].ADA-deficient mice were generated as described previously [39].

Administration of siRNA nanoparticies in vivo:

Bleomycin pulmonary fibrosis model: On Days 2, 5, 12 after bleomycintreatment, each siRNA nanoparticle group is administered either IV or ITat 3 different dose levels of siRNA: 0.15 mg/kg (3 ug/mouse), 0.5 mg/kg(10 ug/mouse), and 1.5 mg/kg (30 ug/mouse). Animal groups (n=3/group)are: 1) control (C57BL/6 mice with one IT instillation of saline); 2)Bleomycin (C57BL/6 mice with one TT instillation of bleomycin); 3)Scrambled IV (bleomycin mice treated IV with 3 doses of nanoparticlescarrying scrambled siRNA); 4) Scrambled IT; 5-14) siRNA IV (estimated 4individual siRNAs and 6 different siRNA combinations, total of 10 siRNAtreatment groups treated IV at 3 dose levels—1 animal/level): 15-24)siRNA IT. Total animal number: 3×24 group=72 C57BL/6 mice.

ADA-null mice: On Days 2, 5, 12 after birth, the mice are treated IVwith different siRNA nanoparticles at 3 dose levels: 0.15 mg/kg, 0.5mg/kg, and 1.5 mg/kg. Animal groups with ADA-null mice (n=3/group) aretreated with: 1) Saline; 2) Scrambled siRNA; 3-12) siRNA (10 siRNAnanoparticle groups at 3 dose levels-1 animal/level). Total animalnumber: 3×12 groups=36 ADA-null mice.

Collection and Processing of Samples: For bleomycin-treated mice, allmice will be sacrificed on Day 23, and the lung samples are collected.The left lungs are fixed by 4% formalin and used for furtherhistological analysis. The right lungs are minced to small pieces anddivided for RNA extraction and collagen content analysis. For ADA-nullmice, all mice will be sacrificed on Day 23 after birth, and the lung,skin and liver are collected and analyzed for histology, RNA andcollagen protein levels.

Analysis: Samples harvested from mice treated with scrambled or testsiRNA, are analyzed for target gene down regulation by real time RT-PCRfor RNA levels and by western blot for protein expression. Collagen isvisualized using H&E and Masson's trichrome staining, and measured withSircol colorimetric assay (Biocolor, Belfast, UK) following methodpreviously described [29].

Outcomes: The comparison of mRNA and protein expression profiles betweencontrol, bleomycin-treated, and siRNA treated C57BL/6 mice will revealkey fibrotic genes and their interactions. Treatment with siRNAnanoparticles by IV or IT will significantly down regulate the mRNA andprotein levels of target genes and potentially other fibrotic genes in adose-dependent manner. Robust knockdown of key fibrotic genes will becorrelated with significant reduction of collagen deposition, asdemonstrated both by histology and collagen content measurement.Survival of ADA-null mice may potentially be prolonged by siRNAnanoparficie treatment. The 3 most effective siRNA nanoparticlecombinations will be selected for expanded efficacy testing in Example5.

Example 6

This example provides information to show the In Vivo Evaluation ofSafety and Anti-fibrosis Efficacy of Selected siRNA Combinations

The in vivo safety and anti-fibrosis efficacy of 3 selected siRNAcombinations will be evaluated in bleomycin pulmonary fibrosis andADA-null mouse models. Preliminary study in Example 5 will suggest the 3most effective siRNA nanoparticle combinations and a safe dose for invivo delivery via IV and IT routes. The study in this aim seeks todemonstrate the safety and efficacy of the selected siRNA combinationswith a longer repeated treatment and narrow to 1 optimal siRNAcombination for further development into a potential therapeutic agent.

Mouse fibrosis models: Bleomycin-induced pulmonary fibrosis model andADA-deficient mice are described in Example 5.

Administration of siRNA nanoparticles in vivo:

Bleomycin pulmonary fibrosis model: On Days 2, 5, 12, 19, 26 afterbleomycin treatment, mice will be treated with the selected siRNAcombinations at dose determined in Example 5. Mice are monitored forweight loss and signs of toxicity following siRNA treatment. Animalgroups (n=8/group) are: 1) control; 2) Bleomycin; 3) Scrambled IV; 4)Scrambled IT; 5-7) siRNA IV; 8-10) siRNA IT. Total animal number: 8×10group=80 C57BL/6 mice.

ADA-null mice: On Days 2, 5, 12 after birth, the mice are treated IVwith the selected siRNA combinations at dose determined in Example 4.Mice are monitored for weight loss and signs of toxicity following siRNAtreatment. Animal groups with ADA-null mice (n=8/group) are treatedwith: 1) Saline; 2) Scrambled siRNA; 3-5) siRNA, Total animal number:8×5 groups=40 ADA-null mice.

Collection and Processing of Samples: Sample collection and processingwill be at Day 36 follow method outlined in the Example 4.

Analysis: Samples analysis will follow method outlined in Example 5.

Outcomes: The results from this study will in general agree withpreliminary data from Example 4. The knockdown of target and otherfibrotic genes will correlate with anti-fibrotic efficacy as shown bydecrease in collagen deposition in fibrosis lesions as shown byhistological analysis and collagen content measurement. The siRNAcombination most effective in decreasing levels of key fibrotic genesand reducing fibrosis in the 2 mouse fibrosis models will be selectedfor further development into a therapeutic agent for human fibroticdiseases.

Example 7

This example provides information to show the increased stability ofPeptide-plasmid DNA Nanoparticles

The peptide-plasmid nanoparticles were prepared by mixing amphipathicpeptide and plasmid. Stock solutions of amphipathic peptide are preparedat 1 mg/mL in distilled water and sonicated for 10 min. Stock solutionsof plasmid are prepared at 100 μM concentrations in 50 mM Tris, 0.5 mMEDTA buffer. Peptide/plasmid complexes or nanoparticies are formed inpure water by incubating peptide (373 μM stock solution) with plasmid(100 μM stock solution) for 30 mm at 37 C with final molar ratio ofpeptide and plasmid at 10:1 or 20:1. The plasmid alone and thepeptide/plasmid complex are stored in PBS for 1 week at 40 C to test thestability of the plasmid. The percentage of superceded DNA is measuredafter 1 week using agarose gel electrophoresis using standard techniques(see for example—Pillai V B, Hellerstein M, Yu T, Amara R R, Robinson HL. Comparative studies on in vitro expression and in vivo immunogenicityof supercoiled and open circular forms of plasmid DNA vaccines. Vaccine.2008 Feb. 20;26(8):1136-41). It takes approximately 7 days for 95%supercoiled DNA in PBS to reach 80% supercoil at 40 C. In the case ofthe peptide-plasmid complex, the level of supercoil is maintained >90%at 1 week.

Example 8

This example provides information to show the treatment of a cancer withfibrosis and inflammation (pancreatic cancer) with selected siRNAcombinations

Pancreatic cancer and some other cancers are known to have a fibrotic ordesmoplastic stroma. However there have been no studies to specificallytarget the stromal components of pancreatic cancer. Peptide basednanoparticles containing siRNA targeted to CTGF, SPARC, TIMPs, TGFbeta1or 2, MMPs and beta-catenin were prepared as described above andadministered to athymic mice with direct from patient pancreaticxenografts or used in genetically engineered mice that spontaneouslydevelop pancreatic cancer. Intravenous administration was initiated oncetumors were detectable. Animals were treated every 4 days for 5treatments along with a control group. Tumor size was monitoredthroughout the course of the study and tumor histology was determinedafter 5 treatments. A significant reduction in the stromal components,in particular collagen was observed after treatment.

LIST OF REFERENCES

Which are incorporated herein in their entirety for all uses:

A publication by Cronstein [2011, http://f1000.com/reports/b/3/21;http://f1000.com/reports/b/3/21/pdf] highlights the importance ofAdenosine receptors and fibrosis is incorporated herein by reference inits entirety.

Attenuation of fibrosis in vitro and in vivo with SPARC siRNA:. Apublication by Wang et al (Arthritis Res Ther. 2010;12(2):R60. Epub 2010Apr. 1.) highlights the importance of SPARC and fibrosis and isincorporated by reference herein in its entirety.

Attenuation of expression of extracellular matrix genes with siRNAs toSparc and Ctgf in skin fibroblasts of CTGF transgenic mice. Apublication by Wang et al. (Int J Immunopathol Pharmacol. 2011July-September;24(3):595-601) highlights the importance of SPARC andfibrosis and is incorporated by reference herein in its entirety.

SPARC Suppresses Apoptosis of Idiopathic Pulmonary Fibrosis Fibroblaststhrough Constitutive Activation of beta-Catenin: A publication by Changet al [The Journal of Biological Chemistry, Vol. 285, NO. 11, pp.8196-8206, Mar. 12, 2010] highlights the relevance of SPARC in pulmonaryfibrosis and is incorporated by reference herein in its entirety.

Secreted Protein Acidic And Rich In Cysteine (spare) Expression IsRegulated By Selectively Tgf-Beta Via Pi3k Signaling: A publication byS, Shibatal, J. Ishiyamal, K. Hagiharal, K. Murakami (Am J Respir CritCare Med 183;2011:A3478) is incorporated by reference herein in itsentirety.

Adenovirus-mediated inhibition of SPARC attenuates liver fibrosis inrats: Camino A M, Atorrasagasti C, Maccio D, Prada F, Salvatierra E,Rizzo M, Alaniz L, Aquino J B, Podhajeer O L, Silva M, Mazzolini G. [JGene Med. 2008 September;10(9):993-1004.] the contents of thispublication are incorporated herein in its entirety.

TGF-beta and fibrosis in different organs—molecular pathway imprints:Pohlers D, Brenmoehl J, Löffler I, Müller C K, Leipner C,Schultze-Mosgau S, Stallmach A, Kinne R W, Wolf G. [Biochim BiophysActa, 2009 August;1792(8):746-56. Epub 2009 Jun. 17] the contents ofthis publication are incorporated herein in its entirety.

TGF-beta1 Gene Silencing for Treating Liver Fibrosis: (Kun Cheng,Ningning Yang and Ram I. Mahato: Mol. Pharmaceutics, 2009, 6 (3), pp772-779)—the contents of this publication are incorporated herein in itsentirety.

Fibrotic disease: A pair of novel targets: Charlotte Harrison [NatureReviews Drug Discovery 8, 773 (October 2009)|doi:10.1038/nrd3005] thecontents of this publication are incorporated herein in its entirety.

Potential Therapeutic Targets for Cardiac Fibrosis: TGFbeta,Angiotensin, Endothelin, CCN2 (CTGF), and PDGF, Partners in FibroblastActivation. Andrew Leask [Circulation Research. 2010; 106: 1675-1680]the contents of this publication are incorporated herein in itsentirety.

Small interfering RNAs (siRNAs) targeting TGF-beta1 mRNA suppressasbestos-induced expression of TGF-beta1 and CTGF in fibroblasts: (Lai TC, Pociask D A, Ferris M, Nguyen H T, Miller C A, Brody A, Sullivan D; JEnviron Pathol Toxicol Oncol. 2009. 28(2):109-19) the contents of thispublication are incorporated herein in its entirety.

Inhibition of TGF-beta receptor 1 by siRNA suppresses the motility andinvasiveness of T24 bladder cancer cells via modulation of integrins andmatrix metalloproteinase: Li Y, Yang K, Mao Q, Zheng X, Kong D, Xie L;Int Urol Nephrol, 2010 June;42(2):315-23. Epub 2009 Aug. 8. the contentsof this publication are incorporated herein in its entirety

Modulation of collagen synthesis in keloid fibroblasts by silencingSmad2 with siRNA: Plast Reconstr Surg. 2006 November:118(6):1328-37. GaoZ, Wang Z, Shi Y, Lin Z, Jiang H, Hou T, Wang Q, Yuan X, Zhao Y, Wu H,Jin Y . the contents of this publication are incorporated herein in itsentirety.

U.S. Pat. No. 8,067,389 describes Silencing of TGFbeta, type II receptorexpression by specific siRNA sequences, the contents of which areincorporated herein in their entirety.

U.S. Pat. No. 8,003,621 discloses compositions that can include acationic polymeric carriers, targeting agent, and therapeutic agenthaving a therapeutic activity such as inhibiting fibrosis within atarget organ or tissue or inhibiting the growth of a cancer cell, thecontents of which are incorporated herein in their entirety.

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1. A method of treating a fibrotic or inflammatory condition in anindividual, comprising administering to the individual an effectiveamount of a pharmaceutical composition comprising one or more nucleicacids that modulate the expression of two or more genes involved in thedevelopment or progression of fibrosis or inflammation.
 2. The method ofclaim 1, wherein the two or more genes are selected from the groupconsisting of CTGF(CCN2), TGFbetai, TGFbeta receptor 1, TGFbeta receptor2, TGFbeta receptor 3, beta-catenin, SPARC, VEGF, Angiotensin II, TIMP,HSP47, thrombospondin, CCN1, LOXL2, MMP2, MMP9, CCL2, Adenosine receptorA2A, Adenosine receptor A2B, Adenylyl cyclase, Smad 3, Smad 4, Smad 7,SOX9, arrestin, PDCD4, PAI-1, NF-kB, and PARP-1 GAD65, sGAD65, BAX, p53PTEN, STAT5, smoothened, GLI1, GLI2, and Patched-1.
 3. A method oftreating a fibrotic or inflammatory condition in an individual,comprising administering to the individual an effective amount of apharmaceutical composition comprising one or more active agents thatmodulate the activity or expression of two or more genes involved in thedevelopment or progression of fibrosis or inflammation, selected from,CTGF(CCN2), TGFbetai, TGFbeta receptor 1, TGFbeta receptor 2, TGFbetareceptor 3, beta-catenin, SPARC, VEGF, Angiotensin II, TIMP, HSP47,thrombospondin, CCN1, LOXL2, MMP2, MMP9, CCL2, Adenosine receptor A2A,Adenosine receptor A2B, Adenylyl cyclase, Smad 3, Smad 4, Smad 7, SOX9,arrestin, PDCD4, PAI-1, NF-kB, and PARP-1 GAD65, sGAD65, BAX, p53 PTEN,STAT5, smoothened, GLI1, GLI2, Patched-1.
 4. The method of claim 3,wherein the one or more active agents are nucleic acids.
 5. The methodof claim 4, wherein at least one of the nucleic acids is a singlestranded oligonucleotide.
 6. The method of claim 4, wherein at least oneof the nucleic acids is a double stranded oligonucleotide.
 7. The methodof claim 4, wherein at least one of the nucleic acids Is selected fromthe group consisting of antisense oligonucleotide, RNAi, shRNA, siRNA,miRNA, or plasmid DNA. 8-10. (canceled)
 11. The method of claim 4,wherein at least one of the nucleic acids is about 10 to about 50nucleotides long.
 12. The method of claim 4, wherein the compositioncomprises two or more nucleic acids.
 13. The method of claim 12, whereinthe two or more nucleic acids are of the same kind.
 14. The method ofclaim 12, wherein the two or more nucleic acids are of different kinds.15. The method of claim 12, wherein the composition comprises twonucleic acids, and wherein the molar ratio of the two nucleic acids isabout 0.1:1 to about 10:1.
 16. The method of claim 12, wherein the twoor more nucleic acids in the pharmaceutical composition are in equalmolar proportions.
 17. The method of claim 12, wherein the nucleic acidsare associated with a carrier molecule. 18-19. (canceled)
 20. The methodof claim 17, wherein the carrier molecule is selected from the groupconsisting of a peptide, a protein, an antibody, a lipid, aphospholipid, a polymer, an aptamer, a nanoparticle, a liposome, adendrimer, a polymerosome, a viral vector, and a micelle. 21-34.(canceled)
 35. A pharmaceutical composition comprising two or moreactive agents that modulate the expression of two or more genes involvedin the development or progression of fibrosis or inflammation. 36-59.(canceled)